Chemostat Studies of TCE-Dehalogenating Anaerobic Consortia under Excess and Limited Electron Donor Addition

NASA Astrophysics Data System (ADS)

Semprini, L.; Azizian, M.; Green, J.; Mayer-Blackwell, K.; Spormann, A. M.

2015-12-01

Two cultures - the Victoria Strain (VS) and the Evanite Strain (EV), enriched with the organohalide respiring bacteria Dehalococcoides mccartyi - were grown in chemostats for more than 4 years at a mean cell residence time of 50 days. The slow doubling rate represents growth likely experienced in the subsurface. The chemostats were fed formate as an electron donor and trichloroethene (TCE) as the terminal electron acceptor. Under excess formate conditions, stable operation was observed with respect to TCE transformation, steady-state hydrogen (H2) concentrations (40 nM), and the structure of the dehalogenating community. Both cultures completely transformed TCE to ethene, with minor amounts of vinyl chloride (VC) observed, along with acetate formation. When formate was limited, TCE was transformed incompletely to ethene (40-60%) and VC (60- 40%), and H2 concentrations ranged from 1 to 3 nM. The acetate concentration dropped below detection. Batch kinetic studies of TCE transformation with chemostat harvested cells found transformation rates of c-DCE and VC were greatly reduced when the cells were grown with limited formate. Upon increasing formate addition to the chemostats, from limited to excess, essentially complete transformation of TCE to ethene was achieved. The increase in formate was associated with an increase in H2 concentration and the production of acetate. Results of batch kinetic tests showed increases in transformation rates for TCE and c-DCE by factors of 3.5 and 2.5, respectively, while VC rates increased by factors of 33 to 500, over a six month period. Molecular analysis of chemostat samples is being performed to quantify the changes in copy numbers of reductase genes and to determine whether shifts in the strains of Dehalococcoides mccartyi where responsible for the observed rate increases. The results demonstrate the importance of electron donor supply for successful in-situ remediation.

INFLUENCE OF HYDRAULIC RETENTION TIME ON EXTENT OF PCE DECHLORINATION AND PRELIMINARY CHARACTERIZATION OF THE ENRICHMENT CULTURE. (R826694C703)

EPA Science Inventory

The extent of tetrachloroethene (PCE) dechlorination in two chemostats was evaluated as a function of hydraulic retention time (HRT). The inoculum of these chemostats was from an upflow anaerobic sludge blanket (UASB) reactor that rapidly converts PCE to vinyl chloride (VC) an...

A Simulator-Assisted Workshop for Teaching Chemostat Cultivation in Academic Classes on Microbial Physiology.

PubMed

Hakkaart, Xavier D V; Pronk, Jack T; van Maris, Antonius J A

2017-01-01

Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under tightly defined conditions, provides a powerful platform to teach key features of microbial growth and metabolism. Substrate-limited chemostat cultivation can be mathematically described by four equations. These encompass mass balances for biomass and substrate, an empirical relation that describes distribution of consumed substrate over growth and maintenance energy requirements (Pirt equation), and a Monod-type equation that describes the relation between substrate concentration and substrate-consumption rate. The authors felt that the abstract nature of these mathematical equations and a lack of visualization contributed to a suboptimal operative understanding of quantitative microbial physiology among students who followed their Microbial Physiology B.Sc. courses. The studio-classroom workshop presented here was developed to improve student understanding of quantitative physiology by a set of question-guided simulations. Simulations are run on Chemostatus, a specially developed MATLAB-based program, which visualizes key parameters of simulated chemostat cultures as they proceed from dynamic growth conditions to steady state. In practice, the workshop stimulated active discussion between students and with their teachers. Moreover, its introduction coincided with increased average exam scores for questions on quantitative microbial physiology. The workshop can be easily implemented in formal microbial physiology courses or used by individuals seeking to test and improve their understanding of quantitative microbial physiology and/or chemostat cultivation.

Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat.

PubMed

Jeong, Haeyoung; Lee, Sang J; Kim, Pil

2016-09-20

Natural evolution involves genetic diversity such as environmental change and a selection between small populations. Adaptive laboratory evolution (ALE) refers to the experimental situation in which evolution is observed using living organisms under controlled conditions and stressors; organisms are thereby artificially forced to make evolutionary changes. Microorganisms are subject to a variety of stressors in the environment and are capable of regulating certain stress-inducible proteins to increase their chances of survival. Naturally occurring spontaneous mutations bring about changes in a microorganism's genome that affect its chances of survival. Long-term exposure to chemostat culture provokes an accumulation of spontaneous mutations and renders the most adaptable strain dominant. Compared to the colony transfer and serial transfer methods, chemostat culture entails the highest number of cell divisions and, therefore, the highest number of diverse populations. Although chemostat culture for ALE requires more complicated culture devices, it is less labor intensive once the operation begins. Comparative genomic and transcriptome analyses of the adapted strain provide evolutionary clues as to how the stressors contribute to mutations that overcome the stress. The goal of the current paper is to bring about accelerated evolution of microorganisms under controlled laboratory conditions.

Kinetics of styrene biodegradation by Pseudomonas sp. E-93486.

PubMed

Gąszczak, Agnieszka; Bartelmus, Grażyna; Greń, Izabela

2012-01-01

The research into kinetics of styrene biodegradation by bacterial strain Pseudomonas sp. E-93486 coming from VTT Culture Collection (Finland) was presented in this work. Microbial growth tests in the presence of styrene as the sole carbon and energy source were performed both in batch and continuous cultures. Batch experiments were conducted for initial concentration of styrene in the liquid phase changed in the range of 5-90 g m(-3). The Haldane model was found to be the best to fit the kinetic data, and the estimated constants of the equation were: μ (m) = 0.1188 h(-1), K(S) = 5.984 mg l(-1), and K (i) = 156.6 mg l(-1). The yield coefficient mean value [Formula in text] for the batch culture was 0.72 g(dry cells weight) (g(substrate))(-1). The experiments conducted in a chemostat at various dilution rates (D = 0.035-0.1 h(-1)) made it possible to determine the value of the coefficient for maintenance metabolism m (d) = 0.0165 h(-1) and the maximum yield coefficient value [Formula in text]. Chemostat experiments confirmed the high value of yield coefficient [Formula in text] observed in the batch culture. The conducted experiments showed high activity of the examined strain in the styrene biodegradation process and a relatively low sensitivity to inhibition of its growth at higher concentrations of styrene in the solution. Such exceptional features of Pseudomonas sp. E-93486 make this bacterial strain the perfect candidate for technical applications.

Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes

PubMed Central

Baart, Gino JE; Zomer, Bert; de Haan, Alex; van der Pol, Leo A; Beuvery, E Coen; Tramper, Johannes; Martens, Dirk E

2007-01-01

Background Neisseria meningitidis is a human pathogen that can infect diverse sites within the human host. The major diseases caused by N. meningitidis are responsible for death and disability, especially in young infants. In general, most of the recent work on N. meningitidis focuses on potential antigens and their functions, immunogenicity, and pathogenicity mechanisms. Very little work has been carried out on Neisseria primary metabolism over the past 25 years. Results Using the genomic database of N. meningitidis serogroup B together with biochemical and physiological information in the literature we constructed a genome-scale flux model for the primary metabolism of N. meningitidis. The validity of a simplified metabolic network derived from the genome-scale metabolic network was checked using flux-balance analysis in chemostat cultures. Several useful predictions were obtained from in silico experiments, including substrate preference. A minimal medium for growth of N. meningitidis was designed and tested succesfully in batch and chemostat cultures. Conclusion The verified metabolic model describes the primary metabolism of N. meningitidis in a chemostat in steady state. The genome-scale model is valuable because it offers a framework to study N. meningitidis metabolism as a whole, or certain aspects of it, and it can also be used for the purpose of vaccine process development (for example, the design of growth media). The flux distribution of the main metabolic pathways (that is, the pentose phosphate pathway and the Entner-Douderoff pathway) indicates that the major part of pyruvate (69%) is synthesized through the ED-cleavage, a finding that is in good agreement with literature. PMID:17617894

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

N'Guessan, L.A.; Elifantz, H.; Nevin, K.P.

2009-09-01

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript levels in G.more » sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve due to the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.« less

Molecular Analysis of Phosphate Limitation in Geobacteraceae During the Bioremediation of a Uranium-Contaminated Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

N'Guessan, A. Lucie; Elifantz, H.; Nevin, Kelly P.

2010-02-01

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript levels in G.more » sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve due to the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.« less

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

N'Guessan, A. Lucie; Elifantz, H.; Nevin, Kelly P.

2010-01-10

Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphatelimitation were identified by microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high-affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU upregulated the most. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducensmore » grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium-bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve because of the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.« less

Mixotrophic and autotrophic growth of Thiobacillus acidophilus on glucose and thiosulfate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pronk, J.T.; Meulenberg, R.; van den Berg, D.J.C.

1990-11-01

Mixotrophic growth of the facultatively autotrophic acidophile Thiobacillus acidophilus on mixtures of glucose and thiosulfate or tetrathionate was studied in substrate-limited chemostat cultures. Growth yields in mixotrophic cultures were higher than the sum of the heterotrophic and autographic growth yields. Pulse experiments with thiosulfate indicated that tetrathionate is an intermediate during thiosulfate oxidation by cell suspensions of T. acidophilus. From mixotrophic growth studied, the energetic value of thiosulfate and tetrathionate redox equivalents was estimated to be 50% of that of redox equivalents derived from glucose oxidation. Ribulose 1,5-bisphosphate carboxylase (RuBPCase) activities in cell extracts and rates of sulfur compound oxidationmore » by cell suspensions increased with increasing thiosulfate/glucose ratios in the influent medium of the mixotrophic cultures. Significant RuBPCase and sulfur compound-oxidizing activities were detected in heterotrophically grown T. acidophilus. Polyhedral inclusion bodies (carboxysomes) could be observed at low frequencies in thin sections of cells grown in heterotrophic, glucose-limited chemostat cultures. Highest RuBPCase activities and carboxysome abundancy were observed in cells from autotrophic, CO{sub 2}-limited chemostat cultures. The maximum growth rate at which thiosulfate was still completely oxidized was increased when glucose was utilized simultaneously. This, together with the fact that even during heterotrophic growth the organism exhibited significant activities of enzymes involved in autotrophic metabolism, indicates that T. acidophilus is well adapted to a mixotrophic lifestyle. In this respect, T. acidophilus may have a competitive advantage over autotrophic acidophiles with respect to the sulfur compound oxidation in environments in which organic compounds are present.« less

Major role of nutrient supply in the control of picophytoplankton community structure

NASA Astrophysics Data System (ADS)

Mouriño, B.; Agusti, S.; Bode, A.; Cermeno, P.; Chouciño, P.; da Silva, J. C. B.; Fernández-Castro, B.; Gasol, J.; Gil Coto, M.; Graña, R.; Latasa, M.; Lubián, L.; Marañón, E.; Moran, X. A.; Moreno, E.; Moreira-Coello, V.; Otero-Ferrer, J. L.; Ruiz Villarreal, M.; Scharek, R.; Vallina, S. M.; Varela, M.; Villamaña, M.

2016-02-01

The Margalef's mandala (1978) is a simplified bottom-up control model that explains how mixing and nutrient concentration determine the composition of marine phytoplankton communities. Due to the difficulties of measuring turbulence in the field, previous attempts to verify this model have applied different proxies for nutrient supply, and very often used interchangeably the terms mixing and stratification. Moreover, because the mandala was conceived before the discovery of smaller phytoplankton groups (picoplankton <2 μm), it describes only the succession of vegetative phases of microplankton. In order to test the applicability of the classical mandala to picoplankton groups, we used a multidisciplinary approach including specifically designed field observations supported by remote sensing, database analyses, and modeling and laboratory chemostat experiments. Simultaneous estimates of nitrate diffusive fluxes, derived from microturbulence observations, and picoplankton abundance collected in more than 200 stations, spanning widely different hydrographic regimes, showed that the contribution of eukaryotes to picoautotrophic biomass increases with nutrient supply, whereas that of picocyanobacteria shows the opposite trend. These findings were supported by laboratory and modeling chemostat experiments that reproduced the competitive dynamics between picoeukaryote sand picocyanobacteria as a function of changing nutrient supply. Our results indicate that nutrient supply controls the distribution of picoplankton functional groups in the ocean, further supporting the model proposed by Margalef.

Combinatorial influence of environmental parameters on transcription factor activity.

PubMed

Knijnenburg, T A; Wessels, L F A; Reinders, M J T

2008-07-01

Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in unraveling these transcription regulation networks, the actual environmental signals are often not incorporated into the model, simply because they have not been measured. The unquantified heterogeneity of the environmental parameters across microarray experiments frustrates regulatory network inference. We propose an inference algorithm that models the influence of environmental parameters on gene expression. The approach is based on a yeast microarray compendium of chemostat steady-state experiments. Chemostat cultivation enables the accurate control and measurement of many of the key cultivation parameters, such as nutrient concentrations, growth rate and temperature. The observed transcript levels are explained by inferring the activity of TFs in response to combinations of cultivation parameters. The interplay between activated enhancers and repressors that bind a gene promoter determine the possible up- or downregulation of the gene. The model is translated into a linear integer optimization problem. The resulting regulatory network identifies the combinatorial effects of environmental parameters on TF activity and gene expression. The Matlab code is available from the authors upon request. Supplementary data are available at Bioinformatics online.

Numerical proof for chemostat chaos of Shilnikov's type.

PubMed

Deng, Bo; Han, Maoan; Hsu, Sze-Bi

2017-03-01

A classical chemostat model is considered that models the cycling of one essential abiotic element or nutrient through a food chain of three trophic levels. The long-time behavior of the model was known to exhibit complex dynamics more than 20 years ago. It is still an open problem to prove the existence of chaos analytically. In this paper, we aim to solve the problem numerically. In our approach, we introduce an artificial singular parameter to the model and construct singular homoclinic orbits of the saddle-focus type which is known for chaos generation. From the configuration of the nullclines of the equations that generates the singular homoclinic orbits, a shooting algorithm is devised to find such Shilnikov saddle-focus homoclinic orbits numerically which in turn imply the existence of chaotic dynamics for the original chemostat model.

Concentration-discharge relationships in headwater streams of the Sierra Nevada, California

NASA Astrophysics Data System (ADS)

Hunsaker, Carolyn T.; Johnson, Dale W.

2017-09-01

We examined stream water concentration-discharge relationships for eight small, forest watersheds ranging in elevation from 1485 to 2465 m in the southern Sierra Nevada. These headwater streams revealed nearly chemostatic behavior by current definitions for K+, Ca2+, Mg2+, Na+, Cl-, and SO42- in most cases but not for NH4+, NO3-, or ortho-P. The latter ions were somewhat enriched during high flows. All ions studied showed a dilution process at lower flows (<50 L s-1) with the concentration-discharge relationship being more chemostatic at higher flows. While previous studies in the Sierra Nevada have reported peak concentrations of NH4+, NO3-, and SO42- during snowmelt, the headwater systems of the Kings River Experimental Watersheds experience peak concentrations of these ions during the fall rains after the dry summer. These forested watersheds span the rain-snow transition zone, are 49-228 ha in size, and have soils derived from granite. A statistically significant relationship between soils and stream water concentrations for ortho-P, Ca2+, and Na+ strongly suggests that soil chemistry has a major influence on stream water chemistry. Factors controlling stream water NH4+, NO3-, and SO42- concentrations are less clear, but one possible source of spikes in these ions during storm events is input from O-horizon runoff where high concentrations were measured. Overall, stream water concentration-discharge relationships for these Sierran watersheds are similar to those found in other watershed systems (nearly chemostatic); however, the dominant processes controlling these relationships are probably localized because of different watershed characteristics like soil chemistry, vegetation cover, hydrologic flow paths, and weather patterns.

Glucans monomer-exchange dynamics as an open chemical network

NASA Astrophysics Data System (ADS)

Rao, Riccardo; Lacoste, David; Esposito, Massimiliano

2015-12-01

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.

Glucans monomer-exchange dynamics as an open chemical network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Riccardo, E-mail: riccardo.rao@uni.lu; Esposito, Massimiliano, E-mail: massimiliano.esposito@uni.lu; Lacoste, David

2015-12-28

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification

PubMed Central

Knibbe, Carole; Schneider, Dominique; Beslon, Guillaume

2017-01-01

Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character displacement, at the level of the metabolic network but also of the genome structure. This difference of genome structure between both ecotypes impacts the stability of the cross-feeding interaction, when the population is propagated in chemostat conditions. This study shows the crucial role played by seasonality in temporal niche partitioning and in promoting cross-feeding subgroups into stable ecotypes, a premise to sympatric speciation. PMID:28358919

Combinatorial influence of environmental parameters on transcription factor activity

PubMed Central

Knijnenburg, T.A.; Wessels, L.F.A.; Reinders, M.J.T.

2008-01-01

Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in unraveling these transcription regulation networks, the actual environmental signals are often not incorporated into the model, simply because they have not been measured. The unquantified heterogeneity of the environmental parameters across microarray experiments frustrates regulatory network inference. Results: We propose an inference algorithm that models the influence of environmental parameters on gene expression. The approach is based on a yeast microarray compendium of chemostat steady-state experiments. Chemostat cultivation enables the accurate control and measurement of many of the key cultivation parameters, such as nutrient concentrations, growth rate and temperature. The observed transcript levels are explained by inferring the activity of TFs in response to combinations of cultivation parameters. The interplay between activated enhancers and repressors that bind a gene promoter determine the possible up- or downregulation of the gene. The model is translated into a linear integer optimization problem. The resulting regulatory network identifies the combinatorial effects of environmental parameters on TF activity and gene expression. Availability: The Matlab code is available from the authors upon request. Contact: t.a.knijnenburg@tudelft.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18586711

Use of chemostat cultures mimicking different phases of wine fermentations as a tool for quantitative physiological analysis

PubMed Central

2014-01-01

Background Saccharomyces cerevisiae is the most relevant yeast species conducting the alcoholic fermentation that takes place during winemaking. Although the physiology of this model organism has been extensively studied, systematic quantitative physiology studies of this yeast under winemaking conditions are still scarce, thus limiting the understanding of fermentative metabolism of wine yeast strains and the systematic description, modelling and prediction of fermentation processes. In this study, we implemented and validated the use of chemostat cultures as a tool to simulate different stages of a standard wine fermentation, thereby allowing to implement metabolic flux analyses describing the sequence of metabolic states of S. cerevisae along the wine fermentation. Results Chemostat cultures mimicking the different stages of standard wine fermentations of S. cerevisiae EC1118 were performed using a synthetic must and strict anaerobic conditions. The simulated stages corresponded to the onset of the exponential growth phase, late exponential growth phase and cells just entering stationary phase, at dilution rates of 0.27, 0.04, 0.007 h−1, respectively. Notably, measured substrate uptake and product formation rates at each steady state condition were generally within the range of corresponding conversion rates estimated during the different batch fermentation stages. Moreover, chemostat data were further used for metabolic flux analysis, where biomass composition data for each condition was considered in the stoichiometric model. Metabolic flux distributions were coherent with previous analyses based on batch cultivations data and the pseudo-steady state assumption. Conclusions Steady state conditions obtained in chemostat cultures reflect the environmental conditions and physiological states of S. cerevisiae corresponding to the different growth stages of a typical batch wine fermentation, thereby showing the potential of this experimental approach to systematically study the effect of environmental relevant factors such as temperature, sugar concentration, C/N ratio or (micro) oxygenation on the fermentative metabolism of wine yeast strains. PMID:24928139

Catchment chemostasis revisited: water quality responds differently to variations in weather and climate

NASA Astrophysics Data System (ADS)

Godsey, Sarah; Kirchner, James

2017-04-01

Solute concentrations in streamflow typically vary systematically with stream discharge, and the resulting concentration-discharge relationships are important signatures of catchment (bio)geochemical processes. Solutes derived from mineral weathering often exhibit decreasing concentrations with increasing flows, suggesting dilution of a kinetically limited weathering flux by a variable flux of water. However, Godsey et al. (2009) showed that concentration-discharge relationships of weathering-derived solutes in 59 headwater catchments were much flatter than this simple dilution model would predict. Instead, their analysis showed that these catchments behaved almost like chemostats, with rates of solute production and/or mobilization that were nearly proportional to water fluxes, on both event and inter-annual time scales. Here we re-examine these findings using data from roughly 1000 catchments, ranging from ˜10 to >1,000,000 km2 in drainage area, and spanning a wide range of lithologic and climatic settings. Concentration-discharge relationships among this much larger set of much larger catchments are broadly consistent with the chemostatic behavior described by Godsey et al. (2009). Among these same catchments, however, site-to-site variations in mean concentrations are strongly (negatively) correlated with long-term average precipitation and discharge, suggesting strong dilution of stream concentrations under long-term leaching of the critical zone. The picture that emerges is one in which, on event and inter-annual time scales, stream solute concentrations are chemostatically buffered by groundwater storage and fast chemical reactions (such as ion exchange), but on much longer time scales, the catchment's chemostatic "set point" is determined by climatically driven critical zone evolution. Examples illustrating the different influences of (short-term) weather and (long-term) climate on water quality will be presented, and their implications will be discussed. Godsey, S.E., J.W. Kirchner and D.W. Clow, Concentration-discharge relationships reflect chemostatic characteristics of US catchments, Hydrological Processes, 23, 1844-1864, 2009.

Metabolic analyses of the improved ε-poly-L-lysine productivity using a glucose-glycerol mixed carbon source in chemostat cultures.

PubMed

Zhang, Jian-Hua; Zeng, Xin; Chen, Xu-Sheng; Mao, Zhong-Gui

2018-04-21

The glucose-glycerol mixed carbon source remarkably reduced the batch fermentation time of ε-poly-L-lysine (ε-PL) production, leading to higher productivity of both biomass and ε-PL, which was of great significance in industrial microbial fermentation. Our previous study confirmed the positive influence of fast cell growth on the ε-PL biosynthesis, while the direct influence of mixed carbon source on ε-PL production was still unknown. In this work, chemostat culture was employed to study the capacity of ε-PL biosynthesis in different carbon sources at a same dilution rate of 0.05 h -1 . The results indicated that the mixed carbon source could enhance the ε-PL productivity besides the rapid cell growth. Analysis of key enzymes demonstrated that the activities of phosphoenolpyruvate carboxylase, citrate synthase, aspartokinase and ε-PL synthetase were all increased in chemostat culture with the mixed carbon source. In addition, the carbon fluxes were also improved in the mixed carbon source in terms of tricarboxylic acid cycle, anaplerotic and diaminopimelate pathway. Moreover, the mixed carbon source also accelerated the energy metabolism, leading to higher levels of energy charge and NADH/NAD + ratio. The overall improvements of primary metabolism in chemostat culture with glucose-glycerol combination provided sufficient carbon skeletons and ATP for ε-PL biosynthesis. Therefore, the significantly higher ε-PL productivity in the mixed carbon source was a combined effect of both superior substrate group and rapid cell growth.

Microbiological toxicity of tilmicosin on human colonic microflora in chemostats.

PubMed

Hao, Haihong; Yao, Junping; Wu, Qinghua; Wei, Yajing; Dai, Menghong; Iqbal, Zahid; Wang, Xu; Wang, Yulian; Huang, Lingli; Chen, Dongmei; Tao, Yanfei; Liu, Zhenli; Yuan, Zonghui

2015-10-01

To evaluate the microbiological safety of tilmicosin on human intestinal microflora, four chemostat models of healthy human colonic ecosystems were exposed to tilmicosin (0, 0.436, 4.36, and 43.6 μg/mL) for 7 days. Prior to and during drug exposure, three microbiological endpoints were monitored daily including short-chain fatty acids, bacterial counts and macrolide susceptibility. Colonization resistance of each community was determined by 3 successive daily challenges of Salmonella typhimurium. Genes associated with virulence and macrolide resistance in Enterococcus faecalis were determined by PCR. Transcriptional expression of the virulence gene (gelE) in E. faecalis was determined by real-time RT-PCR. Our results showed that different concentrations of tilmicosin did not disrupt the colonization resistance in each chemostat. During exposure to 4.36 and 43.6 μg/mL tilmicosin, the Bacteroides fragilis population was significantly decreased while the proportion of resistant Enterococci increased. After long-term exposure to the highest concentration (43.6 μg/mL) of tilmicosin, the gelE gene was significantly up-regulated in the high-level macrolide resistant strains that also contained the ermB resistance gene. This study was the first of its kind to evaluate the microbiological toxicity of tilmicosin using a chemostat model. These findings also provide new insight into the co-occurrence of macrolide resistance and virulence in E. faecalis under tilmicosin selective pressure. Copyright © 2015 Elsevier Inc. All rights reserved.

Effects of Furfural on the Respiratory Metabolism of Saccharomyces cerevisiae in Glucose-Limited Chemostats

PubMed Central

Sárvári Horváth, Ilona; Franzén, Carl Johan; Taherzadeh, Mohammad J.; Niklasson, Claes; Lidén, Gunnar

2003-01-01

Effects of furfural on the aerobic metabolism of the yeast Saccharomyces cerevisiae were studied by performing chemostat experiments, and the kinetics of furfural conversion was analyzed by performing dynamic experiments. Furfural, an important inhibitor present in lignocellulosic hydrolysates, was shown to have an inhibitory effect on yeast cells growing respiratively which was much greater than the inhibitory effect previously observed for anaerobically growing yeast cells. The residual furfural concentration in the bioreactor was close to zero at all steady states obtained, and it was found that furfural was exclusively converted to furoic acid during respiratory growth. A metabolic flux analysis showed that furfural affected fluxes involved in energy metabolism. There was a 50% increase in the specific respiratory activity at the highest steady-state furfural conversion rate. Higher furfural conversion rates, obtained during pulse additions of furfural, resulted in respirofermentative metabolism, a decrease in the biomass yield, and formation of furfuryl alcohol in addition to furoic acid. Under anaerobic conditions, reduction of furfural partially replaced glycerol formation as a way to regenerate NAD+. At concentrations above the inlet concentration of furfural, which resulted in complete replacement of glycerol formation by furfuryl alcohol production, washout occurred. Similarly, when the maximum rate of oxidative conversion of furfural to furoic acid was exceeded aerobically, washout occurred. Thus, during both aerobic growth and anaerobic growth, the ability to tolerate furfural appears to be directly coupled to the ability to convert furfural to less inhibitory compounds. PMID:12839784

Succinic acid production with Actinobacillus succinogenes: rate and yield analysis of chemostat and biofilm cultures.

PubMed

Brink, Hendrik Gideon; Nicol, Willie

2014-08-19

Succinic acid is well established as bio-based platform chemical with production quantities expecting to increase exponentially within the next decade. Actinobacillus succinogenes is by far the most studied wild organism for producing succinic acid and is known for high yield and titre during production on various sugars in batch culture. At low shear conditions continuous fermentation with A. succinogenes results in biofilm formation. In this study, a novel shear controlled fermenter was developed that enabled: 1) chemostat operation where self-immobilisation was opposed by high shear rates and, 2) in-situ removal of biofilm by increasing shear rates and subsequent analysis thereof. The volumetric productivity of the biofilm fermentations were an order of magnitude more than the chemostat runs. In addition the biofilm runs obtained substantially higher yields. Succinic acid to acetic acid ratios for chemostat runs were 1.28±0.2 g.g(-1), while the ratios for biofilm runs started at 2.4 g.g(-1) and increased up to 3.3 g.g(-1) as glucose consumption increased. This corresponded to an overall yield on glucose of 0.48±0.05 g.g(-1) for chemostat runs, while the yields varied between 0.63 g.g(-1) and 0.74 g.g(-1) for biofilm runs. Specific growth rates (μ) were shown to be severely inhibited by the formation of organic acids, with μ only 12% of μ(max) at a succinic acid titre of 7 g.L(-1). Maintenance production of succinic acid was shown to be dominant for the biofilm runs with cell based production rates (extracellular polymeric substance removed) decreasing as SA titre increases. The novel fermenter allowed for an in-depth bioreaction analysis of A. succinogenes. Biofilm cells achieve higher SA yields than suspended cells and allow for operation at higher succinic acid titre. Both growth and maintenance rates were shown to drastically decrease with succinic acid titre. The A. succinogenes biofilm process has vast potential, where self-induced high cell densities result in higher succinic acid productivity and yield.

A stoichiometric organic matter decomposition model in a chemostat culture.

PubMed

Kong, Jude D; Salceanu, Paul; Wang, Hao

2018-02-01

Biodegradation, the disintegration of organic matter by microorganism, is essential for the cycling of environmental organic matter. Understanding and predicting the dynamics of this biodegradation have increasingly gained attention from the industries and government regulators. Since changes in environmental organic matter are strenuous to measure, mathematical models are essential in understanding and predicting the dynamics of organic matters. Empirical evidence suggests that grazers' preying activity on microorganism helps to facilitate biodegradation. In this paper, we formulate and investigate a stoichiometry-based organic matter decomposition model in a chemostat culture that incorporates the dynamics of grazers. We determine the criteria for the uniform persistence and extinction of the species and chemicals. Our results show that (1) if at the unique internal steady state, the per capita growth rate of bacteria is greater than the sum of the bacteria's death and dilution rates, then the bacteria will persist uniformly; (2) if in addition to this, (a) the grazers' per capita growth rate is greater than the sum of the dilution rate and grazers' death rate, and (b) the death rate of bacteria is less than some threshold, then the grazers will persist uniformly. These conditions can be achieved simultaneously if there are sufficient resources in the feed bottle. As opposed to the microcosm decomposition models' results, in a chemostat culture, chemicals always persist. Besides the transcritical bifurcation observed in microcosm models, our chemostat model exhibits Hopf bifurcation and Rosenzweig's paradox of enrichment phenomenon. Our sensitivity analysis suggests that the most effective way to facilitate degradation is to decrease the dilution rate.

Effect of chloride on ferrous iron oxidation by a Leptospirillum ferriphilum-dominated chemostat culture.

PubMed

Gahan, Chandra Sekhar; Sundkvist, Jan-Eric; Dopson, Mark; Sandström, Ake

2010-06-15

Biomining is the use of microorganisms to catalyze metal extraction from sulfide ores. However, the available water in some biomining environments has high chloride concentrations and therefore, chloride toxicity to ferrous oxidizing microorganisms has been investigated. Batch biooxidation of Fe(2+) by a Leptospirillum ferriphilum-dominated culture was completely inhibited by 12 g L(-1) chloride. In addition, the effects of chloride on oxidation kinetics in a Fe(2+) limited chemostat were studied. Results from the chemostat modeling suggest that the chloride toxicity was attributed to affects on the Fe(2+) oxidation system, pH homeostasis, and lowering of the proton motive force. Modeling showed a decrease in the maximum specific growth rate (micro(max)) and an increase in the substrate constant (K(s)) with increasing chloride concentrations, indicating an effect on the Fe(2+) oxidation system. The model proposes a lowered maintenance activity when the media was fed with 2-3 g L(-1) chloride with a concomitant drastic decrease in the true yield (Y(true)). This model helps to understand the influence of chloride on Fe(2+) biooxidation kinetics. 2010 Wiley Periodicals, Inc.

Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures †

PubMed Central

De Nicola, Raffaele; Hazelwood, Lucie A.; De Hulster, Erik A. F.; Walsh, Michael C.; Knijnenburg, Theo A.; Reinders, Marcel J. T.; Walker, Graeme M.; Pronk, Jack T.; Daran, Jean-Marc; Daran-Lapujade, Pascale

2007-01-01

Transcriptional responses of the yeast Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under limiting and abundant Zn concentrations in chemostat culture. To investigate the context dependency of this transcriptional response and eliminate growth rate-dependent variations in transcription, yeast was grown under several chemostat regimens, resulting in various carbon (glucose), nitrogen (ammonium), zinc, and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified, and the set enabled the definition of the Zn-specific Zap1p regulon, comprised of 26 genes and characterized by a broader zinc-responsive element consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large number of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified. PMID:17933919

Antibiotics in the human food chain: establishing no effect levels of tetracycline, neomycin, and erythromycin using a chemostat model of the human colonic microflora.

PubMed

Carman, Robert J; Simon, Mary Alice; Petzold, H Earl; Wimmer, Robert F; Batra, Monica R; Fernández, A Haydée; Miller, Margaret A; Bartholomew, Mary

2005-11-01

A chemostat model of the healthy human large bowel ecosystem was used to establish no effect levels for tetracycline, neomycin, and erythromycin. For each compound, the equivalent to four oral doses (0, 1.5, 15, and 150 mg/60 kg person/d) was studied. Concentrations of the test compounds in the chemostat medium were intended to simulate fecal levels that might be expected following consumption of food containing antibiotic residue and were based on published oral doses and fecal levels. We monitored the following parameters: short chain fatty acids, bile acids, sulfate reduction, azoreductase and nitroreductase activities, beta-glucosidase and beta-glucuronidase activities, a range of bacterial counts and, lastly, the susceptibility among sentinel bacteria to each test compound. Neomycin and erythromycin reduced bile acid metabolism. Neomycin elevated propionate levels and caused a marginal diminution in azoreductase activity. Based on our results, the no observed effect level (NOEL) of both tetracycline and erythromycin was 15 mg/60 kg person/d. The NOEL for neomycin was 1.5 mg/60 kg person/d.

Impact of solids retention time on dissolved organic nitrogen and its biodegradability in treated wastewater.

PubMed

Simsek, Halis; Kasi, Murthy; Ohm, Jae-Bom; Murthy, Sudhir; Khan, Eakalak

2016-04-01

Dissolved organic nitrogen (DON) and its biodegradability in treated wastewater have recently gained attention due to increased regulatory requirements on effluent quality to protect receiving waters. Laboratory scale chemostat experiments were conducted at 9 different solids retention times (SRTs) (0.3, 0.7, 2, 3, 4, 5, 7, 8, and 13 days) to examine whether SRT could be used to control DON, biodegradable DON (BDON), and DON biodegradability (BDON/DON) levels in treated wastewater. Results indicated no trend between effluent DON and SRTs. Effluent BDON was comparable for SRTs of 0.3-4 days and had a decreasing trend with SRT after that. Effluent DON biodegradability (effluent BDON/effluent DON) ranging from 23% to 59% tended to decrease with SRT. Chemostat during longer SRTs, however, was contributing to non-biodegradable DON (NBDON) and this fraction of DON increased with SRT above 4 days. Model calibration results indicated that ammonification rate, and growth rates for ordinary heterotrophs, ammonia oxidizing bacteria and nitrite oxidizing bacteria were not constants but have a decreasing trend with increasing SRT. This study indicates the benefit of high SRTs in term of producing effluent with less DON biodegradability leading to relatively less oxygen consumption and nutrient support in receiving waters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Physiological, biomass elemental composition and proteomic analyses of Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited chemostat growth

PubMed Central

Folsom, James Patrick

2015-01-01

Escherichia coli physiological, biomass elemental composition and proteome acclimations to ammonium-limited chemostat growth were measured at four levels of nutrient scarcity controlled via chemostat dilution rate. These data were compared with published iron- and glucose-limited growth data collected from the same strain and at the same dilution rates to quantify general and nutrient-specific responses. Severe nutrient scarcity resulted in an overflow metabolism with differing organic byproduct profiles based on limiting nutrient and dilution rate. Ammonium-limited cultures secreted up to 35  % of the metabolized glucose carbon as organic byproducts with acetate representing the largest fraction; in comparison, iron-limited cultures secreted up to 70  % of the metabolized glucose carbon as lactate, and glucose-limited cultures secreted up to 4  % of the metabolized glucose carbon as formate. Biomass elemental composition differed with nutrient limitation; biomass from ammonium-limited cultures had a lower nitrogen content than biomass from either iron- or glucose-limited cultures. Proteomic analysis of central metabolism enzymes revealed that ammonium- and iron-limited cultures had a lower abundance of key tricarboxylic acid (TCA) cycle enzymes and higher abundance of key glycolysis enzymes compared with glucose-limited cultures. The overall results are largely consistent with cellular economics concepts, including metabolic tradeoff theory where the limiting nutrient is invested into essential pathways such as glycolysis instead of higher ATP-yielding, but non-essential, pathways such as the TCA cycle. The data provide a detailed insight into ecologically competitive metabolic strategies selected by evolution, templates for controlling metabolism for bioprocesses and a comprehensive dataset for validating in silico representations of metabolism. PMID:26018546

Concentration-discharge relationships for variably sized streams in Florida: Patterns and drivers in long-term catchment studies

NASA Astrophysics Data System (ADS)

Diamond, J.; Cohen, M.

2012-12-01

Catchment-scale analyses can provide important insight into the processes governing solute sources, transport and storage. Understanding solute dynamics is vital for water management both for accurate predictions of chemical fluxes as well as ecosystem responses to them. This project synthesized long-term (>15 years) hydrochemical data from 80 variably sized (101-105 m2) watersheds in Florida. Our goal was to evaluate scaling effects on flow-solute relationships, and determine the factors that control observed inter-catchment variation. We obtained long term records of a variety of chemical parameters include color, nutrients (N and P), and geogenic solutes (Ca, Si, Mg, Na, Cl) from stations where chemistry and flow data were matched. Catchment attributes (land use, terrain, surface geology) were obtained for each stream as potential covariates. Concentration-discharge relationships were modeled as power functions, the exponents (b) of which were categorized into three end-member scenarios: (1) b>0, or chemodynamic conditions, where increased discharge increases concentration, (2) b=0, or chemostatic conditions, where concentration is independent of discharge, and (3) b<0, or dilution conditions, where increased discharge decreases concentrations. Color was strongly chemodynamic, while geogenic solutes tended to be chemostatic;nutrient-flow relationships varied substantially (from dilution to chemodynamic) suggesting important ancillary controls. To assess between-site variability, power function exponents were compared against land use and catchment area. These results indicate that watersheds dominated by urban land use exhibit stronger dilution effects for most solutes while watersheds dominated by agricultural land use were generally chemostatic particularly for nutrients. This synthesis approach to understanding controls on observed concentration-discharge relationships is crucial to understanding the dynamics and early-warning indicators of anthropogenically-induced transition from dilution to chemostatic behavior.

The establishment of reproducible, complex communities of oral bacteria in the chemostat using defined inocula.

PubMed

McKee, A S; McDermid, A S; Ellwood, D C; Marsh, P D

1985-09-01

Nine commonly isolated oral bacterial populations were inoculated into a glucose-limited and a glucose-excess (amino acid-limited) chemostat maintained at a constant pH 7.0 and a mean community generation time of 13.9 h. The bacterial populations were Streptococcus mutans ATCC 2-27351, Strep. sanguis NCTC 7865, Strep. mitior EF 186, Actinomyces viscosus WVU 627, Lactobacillus casei AC 413, Neisseria sp. A1078, Veillonella alkalescens ATCC 17745, Bacteroides intermedius T 588 and Fusobacterium nucleatum NCTC 10593. All nine populations became established in the glucose-limited chemostat although Strep. sanguis and Neisseria sp. were present only after a second and third inoculation, respectively. In contrast, even following repeated inoculations, Strep. mutans, B. intermedius and Neisseria sp. could not be maintained under glucose-excess conditions. A more extensive pattern of fermentation products and amino acid catabolism occurred under glucose-limited growth; this simultaneous utilization of mixed substrates also contributed to the higher yields (Y molar glucose) and greater species diversity of these communities. Microscopic and biochemical evidence suggested that cell-to-cell interactions and food chains were occurring among community members. To compare the reproductibility of this system, communities were established on three occasions under glucose-limitation and twice under glucose-excess conditions. The bacterial composition of the steady-state communities and their metabolic behaviour were similar when grown under identical conditions but varied in a consistent manner according to the nutrient responsible for limiting growth. Although a direct simulation of the oral cavity was not attempted, the results show that the chemostat could be used as an environmentally-related model to grow complex but reproducible communities of oral bacteria for long periods from a defined inoculum.

Mechanisms for chemostatic behavior in catchments: implications for CO2 consumption by mineral weathering

USGS Publications Warehouse

Clow, David W.; Mast, M. Alisa

2010-01-01

Concentrations of weathering products in streams often show relatively little variation compared to changes in discharge, both at event and annual scales. In this study, several hypothesized mechanisms for this “chemostatic behavior” were evaluated, and the potential for those mechanisms to influence relations between climate, weathering fluxes, and CO2 consumption via mineral weathering was assessed. Data from Loch Vale, an alpine catchment in the Colorado Rocky Mountains, indicates that cation exchange and seasonal precipitation and dissolution of amorphous or poorly crystalline aluminosilicates are important processes that help regulate solute concentrations in the stream; however, those processes have no direct effect on CO2 consumption in catchments. Hydrograph separation analyses indicate that old water stored in the subsurface over the winter accounts for about one-quarter of annual streamflow, and almost one-half of annual fluxes of Na and SiO2 in the stream; thus, flushing of old water by new water (snowmelt) is an important component of chemostatic behavior. Hydrologic flushing of subsurface materials further induces chemostatic behavior by reducing mineral saturation indices and increasing reactive mineral surface area, which stimulate mineral weathering rates. CO2 consumption by carbonic acid mediated mineral weathering was quantified using mass-balance calculations; results indicated that silicate mineral weathering was responsible for approximately two-thirds of annual CO2 consumption, and carbonate weathering was responsible for the remaining one-third. CO2 consumption was strongly dependent on annual precipitation and temperature; these relations were captured in a simple statistical model that accounted for 71% of the annual variation in CO2 consumption via mineral weathering in Loch Vale.

Reproducible Biofilm Cultivation of Chemostat-Grown Escherichia coli and Investigation of Bacterial Adhesion on Biomaterials Using a Non-Constant-Depth Film Fermenter

PubMed Central

Lüdecke, Claudia; Jandt, Klaus D.; Siegismund, Daniel; Kujau, Marian J.; Zang, Emerson; Rettenmayr, Markus; Bossert, Jörg; Roth, Martin

2014-01-01

Biomaterials-associated infections are primarily initiated by the adhesion of microorganisms on the biomaterial surfaces and subsequent biofilm formation. Understanding the fundamental microbial adhesion mechanisms and biofilm development is crucial for developing strategies to prevent such infections. Suitable in vitro systems for biofilm cultivation and bacterial adhesion at controllable, constant and reproducible conditions are indispensable. This study aimed (i) to modify the previously described constant-depth film fermenter for the reproducible cultivation of biofilms at non-depth-restricted, constant and low shear conditions and (ii) to use this system to elucidate bacterial adhesion kinetics on different biomaterials, focusing on biomaterials surface nanoroughness and hydrophobicity. Chemostat-grown Escherichia coli were used for biofilm cultivation on titanium oxide and investigating bacterial adhesion over time on titanium oxide, poly(styrene), poly(tetrafluoroethylene) and glass. Using chemostat-grown microbial cells (single-species continuous culture) minimized variations between the biofilms cultivated during different experimental runs. Bacterial adhesion on biomaterials comprised an initial lag-phase I followed by a fast adhesion phase II and a phase of saturation III. With increasing biomaterials surface nanoroughness and increasing hydrophobicity, adhesion rates increased during phases I and II. The influence of materials surface hydrophobicity seemed to exceed that of nanoroughness during the lag-phase I, whereas it was vice versa during adhesion phase II. This study introduces the non-constant-depth film fermenter in combination with a chemostat culture to allow for a controlled approach to reproducibly cultivate biofilms and to investigate bacterial adhesion kinetics at constant and low shear conditions. The findings will support developing and adequate testing of biomaterials surface modifications eventually preventing biomaterial-associated infections. PMID:24404192

Coliform culturability in over- versus undersaturated drinking waters.

PubMed

Grandjean, D; Fass, S; Tozza, D; Cavard, J; Lahoussine, V; Saby, S; Guilloteau, H; Block, J-C

2005-05-01

The culturability of Escherichia coli in undersaturated drinking water with respect to CaCO3 (corrosive water) or in oversaturated water (non-corrosive water) was tested in different reactors: glass flasks (batch, "non-reactive" wall); glass reactors (chemostat, "non-reactive" wall) versus a corroded cast iron Propella reactor (chemostat, "reactive" wall) and a 15-year-old distribution system pilot (chemostat, "reactive" wall with 1% corroded cast iron and 99% cement-lined cast iron). The E. coli in E. coli-spiked drinking water was not able to maintain its culturability and colonize the experimental systems. It appears from our results that the optimal pH for maintaining E. coli culturability was around 8.2 or higher. However, in reactors with a reactive wall (corroded cast iron), the decline in E. coli culturability was slower when the pH was adjusted to 7.9 or 7.7 (i.e. a reactor fed with corrosive water; pHpHs). We tentatively deduce that corrosion products coming from chemical reactions driven by corrosive waters on the pipe wall improve E. coli culturability.

Transcriptome and proteome dynamics in chemostat culture reveal how Campylobacter jejuni modulates metabolism, stress responses and virulence factors upon changes in oxygen availability

PubMed Central

Guccione, Edward J.; Kendall, John J.; Hitchcock, Andrew; Garg, Nitanshu; White, Michael A.; Mulholland, Francis; Poole, Robert K.

2017-01-01

Summary Campylobacter jejuni, the most frequent cause of food‐borne bacterial gastroenteritis worldwide, is a microaerophile that has to survive high environmental oxygen tensions, adapt to oxygen limitation in the intestine and resist host oxidative attack. Here, oxygen‐dependent changes in C. jejuni physiology were studied at constant growth rate using carbon (serine)‐limited continuous chemostat cultures. We show that a perceived aerobiosis scale can be calibrated by the acetate excretion flux, which becomes zero when metabolism is fully aerobic (100% aerobiosis). Transcriptome changes in a downshift experiment from 150% to 40% aerobiosis revealed many novel oxygen‐regulated genes and highlighted re‐modelling of the electron transport chains. A label‐free proteomic analysis showed that at 40% aerobiosis, many proteins involved in host colonisation (e.g., PorA, CadF, FlpA, CjkT) became more abundant. PorA abundance increased steeply below 100% aerobiosis. In contrast, several citric‐acid cycle enzymes, the peptide transporter CstA, PEB1 aspartate/glutamate transporter, LutABC lactate dehydrogenase and PutA proline dehydrogenase became more abundant with increasing aerobiosis. We also observed a co‐ordinated response of oxidative stress protection enzymes and Fe‐S cluster biogenesis proteins above 100% aerobiosis. Our approaches reveal key virulence factors that respond to restricted oxygen availability and specific transporters and catabolic pathways activated with increasing aerobiosis. PMID:28892295

Use of a series of chemostat cultures to isolate 'improved' variants of the Quorn mycoprotein fungus, Fusarium graminearum A3/5.

PubMed

Wiebe, M G; Robson, G D; Oliver, S G; Trinci, A P

1994-11-01

Variants (designated A23-S and A24-S) of the Quorn myco-protein fungus, Fusarium graminearum A3/5 were isolated from a series of glucose-limited cultures grown at a dilution rate of 0.18 h-1 for a combined total of 109 d. These variants had unchanged mycelial morphologies but, when grown in mixed culture with the parental strain (A3/5) in glucose-limited chemostat culture at 0.18 h-1, A23-S and A24-S had selection coefficients of 0.013 and 0.017 h-1, respectively, and supplanted A3/5. When a monoculture of A23-S was grown in a glucose-limited culture at a dilution rate of 0.18 h-1, the appearance of highly branched (so-called colonial) mutants was delayed compared with their appearance in chemostat cultures of the parental strain. Furthermore, when a monoculture of A24-S was grown in glucose-limited culture at 0.18 h-1, the appearance of colonial mutants was delayed even further. Thus, it is possible to isolate advantageous (relative to A3/5) variants of F. graminearum A3/5 which have unchanged mycelial morphologies, but in which the appearance of colonial mutants is delayed.

The operating diagram of a model of two competitors in a chemostat with an external inhibitor.

PubMed

Dellal, Mohamed; Lakrib, Mustapha; Sari, Tewfik

2018-05-24

Understanding and exploiting the inhibition phenomenon, which promotes the stable coexistence of species, is a major challenge in the mathematical theory of the chemostat. Here, we study a model of two microbial species in a chemostat competing for a single resource in the presence of an external inhibitor. The model is a four-dimensional system of ordinary differential equations. Using general monotonic growth rate functions of the species and absorption rate of the inhibitor, we give a complete analysis for the existence and local stability of all steady states. We focus on the behavior of the system with respect of the three operating parameters represented by the dilution rate and the input concentrations of the substrate and the inhibitor. The operating diagram has the operating parameters as its coordinates and the various regions defined in it correspond to qualitatively different asymptotic behavior: washout, competitive exclusion of one species, coexistence of the species around a stable steady state and coexistence around a stable cycle. This bifurcation diagram which determines the effect of the operating parameters, is very useful to understand the model from both the mathematical and biological points of view, and is often constructed in the mathematical and biological literature. Copyright © 2018 Elsevier Inc. All rights reserved.

rRNA and Poly-β-Hydroxybutyrate Dynamics in Bioreactors Subjected to Feast and Famine Cycles

PubMed Central

Frigon, Dominic; Muyzer, Gerard; van Loosdrecht, Mark; Raskin, Lutgarde

2006-01-01

Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-β-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological advantage. PMID:16597926

rRNA and poly-beta-hydroxybutyrate dynamics in bioreactors subjected to feast and famine cycles.

PubMed

Frigon, Dominic; Muyzer, Gerard; van Loosdrecht, Mark; Raskin, Lutgarde

2006-04-01

Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-beta-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological advantage.

Cyclic-2,3-diphosphoglycerate levels in Methanobacterium thermoautotrophicum reflect inorganic phosphate availability.

PubMed

Seely, R J; Krueger, R D; Fahrney, D E

1983-11-15

Methanobacterium thermoautotrophicum was grown in phosphate-limited chemostat cultures at a dilution rate corresponding to a doubling time of 13.2 h. The cyclic-2,3-diphospho-D-glycerate content of these cells was 8 to 10-fold lower than that of cells grown in batch cultures having a doubling time of 11.5 h. This metabolite accounted for 5% of cell dry weight during batch growth on 2 mM phosphate. In the chemostat the steady-state concentration of phosphate was 4 microM, showing that this methanogen is adapted to highly efficient growth at low phosphate concentrations. Since growth rates were similar in both cultures, the growth rate clearly does not depend on intracellular levels of cyclic-2,3-diphosphoglycerate.

Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis.

PubMed

Tai, Siew Leng; Daran-Lapujade, Pascale; Walsh, Michael C; Pronk, Jack T; Daran, Jean-Marc

2007-12-01

Effects of suboptimal temperatures on transcriptional regulation in yeast have been extensively studied in batch cultures. To eliminate indirect effects of specific growth rates that are inherent to batch-cultivation studies, genome-wide transcriptional responses to low temperatures were analyzed in steady-state chemostats, grown at a fixed specific growth rate (0.03 h(-1)). Although in vivo metabolic fluxes were essentially the same in cultures grown at 12 and at 30 degrees C, concentrations of the growth-limiting nutrients (glucose or ammonia) were higher at 12 degrees C. This difference was reflected by transcript levels of genes that encode transporters for the growth-limiting nutrients. Several transcriptional responses to low temperature occurred under both nutrient-limitation regimes. Increased transcription of ribosome-biogenesis genes emphasized the importance of adapting protein-synthesis capacity to low temperature. In contrast to observations in cold-shock and batch-culture studies, transcript levels of environmental stress response genes were reduced at 12 degrees C. Transcription of trehalose-biosynthesis genes and intracellular trehalose levels indicated that, in contrast to its role in cold-shock adaptation, trehalose is not involved in steady-state low-temperature adaptation. Comparison of the chemostat-based transcriptome data with literature data revealed large differences between transcriptional reprogramming during long-term low-temperature acclimation and the transcriptional responses to a rapid transition to low temperature.

Chemostat studies of bacteriophage M13 infected Escherichia coli JM109 for continuous ssDNA production.

PubMed

Kick, Benjamin; Behler, Karl Lorenz; Severin, Timm Steffen; Weuster-Botz, Dirk

2017-09-20

Steady state studies in a chemostat enable the control of microbial growth rate at defined reaction conditions. The effects of bacteriophage M13 infection on maximum growth rate of Escherichia coli JM109 were studied in parallel operated chemostats on a milliliter-scale to analyze the steady state kinetics of phage production. The bacteriophage infection led to a decrease in maximum specific growth rate of 15% from 0.74h -1 to 0.63h -1 . Under steady state conditions, a constant cell specific ssDNA formation rate of 0.15±0.004 mg ssDNA g CDW -1 h -1 was observed, which was independent of the growth rate. Using the estimated kinetic parameters for E. coli infected with bacteriophage M13, the ssDNA concentration in the steady state could be predicted as function of the dilution rate and the glucose concentration in the substrate. Scalability of milliliter-scale data was approved by steady state studies on a liter-scale at a selected dilution rate. An ssDNA space-time yield of 5.7mgL -1 h -1 was achieved with increased glucose concentration in the feed at a dilution rate of 0.3h -1 , which is comparable to established fed-batch fermentation with bacteriophage M13 for ssDNA production. Copyright © 2017 Elsevier B.V. All rights reserved.

The acetylation degree of alginates in Azotobacter vinelandii ATCC9046 is determined by dissolved oxygen and specific growth rate: studies in glucose-limited chemostat cultivations.

PubMed

Castillo, Tania; Galindo, Enrique; Peña, Carlos F

2013-07-01

Alginates are polysaccharides that may be used as viscosifiers and gel or film-forming agents with a great diversity of applications. The alginates produced by bacteria such as Azotobacter vinelandii are acetylated. The presence of acetyl groups in this type of alginate increases its solubility, viscosity, and swelling capability. The aim of this study was to evaluate, in glucose-limited chemostat cultivations of A. vinelandii ATCC9046, the influence of dissolved oxygen tension (DO) and specific growth rate (μ) on the degree of acetylation of alginates produced by this bacterium. In glucose-limited chemostat cultivations, the degree of alginate acetylation was evaluated under two conditions of DO (1 and 9 %) and for a range of specific growth rates (0.02-0.15 h⁻¹). In addition, the alginate yields and PHB production were evaluated. High DO in the culture resulted in a high degree of alginate acetylation, reaching a maximum acetylation degree of 6.88 % at 9 % DO. In contrast, the increment of μ had a negative effect on the production and acetylation of the polymer. It was found that at high DO (9 %) and low μ, there was a reduction of the respiration rate, and the PHB accumulation was negligible, suggesting that the flux of acetyl-CoA (the acetyl donor) was diverted to alginate acetylation.

CO2-dependent carbon isotope fractionation in the dinoflagellate Alexandrium tamarense

NASA Astrophysics Data System (ADS)

Wilkes, Elise B.; Carter, Susan J.; Pearson, Ann

2017-09-01

The carbon isotopic composition of marine sedimentary organic matter is used to resolve long-term histories of pCO2 based on studies indicating a CO2-dependence of photosynthetic carbon isotope fractionation (εP). It recently was proposed that the δ13C values of dinoflagellates, as recorded in fossil dinocysts, might be used as a proxy for pCO2. However, significant questions remain regarding carbon isotope fractionation in dinoflagellates and how such fractionation may impact sedimentary records throughout the Phanerozoic. Here we investigate εP as a function of CO2 concentration and growth rate in the dinoflagellate Alexandrium tamarense. Experiments were conducted in nitrate-limited chemostat cultures. Values of εP were measured on cells having growth rates (μ) of 0.14-0.35 d-1 and aqueous carbon dioxide concentrations of 10.2-63 μmol kg-1 and were found to correlate linearly with μ/[CO2(aq)] (r2 = 0.94) in accord with prior, analogous chemostat investigations with eukaryotic phytoplankton. A maximum fractionation (εf) value of 27‰ was characterized from the intercept of the experiments, representing the first value of εf determined for an algal species employing Form II RubisCO-a structurally and catalytically distinct form of the carbon-fixing enzyme. This value is larger than theoretical predictions for Form II RubisCO and not significantly different from the ∼25‰ εf values observed for taxa employing Form ID RubisCO. We also measured the carbon isotope contents of dinosterol, hexadecanoic acid, and phytol from each experiment, finding that each class of biomarker exhibits different isotopic behavior. The apparent CO2-dependence of εP values in our experiments strengthens the proposal to use dinocyst δ13C values as a pCO2 proxy. Moreover, the similarity between the εf value for A. tamarense and the consensus value of ∼25‰ indicates that the CO2-sensitivity of carbon isotope fractionation saturates at similar CO2 levels across all three ecologically prominent clades of eukaryotic phytoplankton. This continuity of εf across taxa may help to explain why there is no coherent signature of phytoplankton evolutionary succession in Phanerozoic carbon isotope records.

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast.

PubMed

Hope, Elyse A; Amorosi, Clara J; Miller, Aaron W; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J

2017-06-01

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1 , and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1 , which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. Copyright © 2017 Hope et al.

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast

PubMed Central

Hope, Elyse A.; Amorosi, Clara J.; Miller, Aaron W.; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J.

2017-01-01

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. PMID:28450459

Comparing the chlorine disinfection of detached biofilm clusters with those of sessile biofilms and planktonic cells in single- and dual-species cultures.

PubMed

Behnke, Sabrina; Parker, Albert E; Woodall, Dawn; Camper, Anne K

2011-10-01

Although the detachment of cells from biofilms is of fundamental importance to the dissemination of organisms in both public health and clinical settings, the disinfection efficacies of commonly used biocides on detached biofilm particles have not been investigated. Therefore, the question arises whether cells in detached aggregates can be killed with disinfectant concentrations sufficient to inactivate planktonic cells. Burkholderia cepacia and Pseudomonas aeruginosa were grown in standardized laboratory reactors as single species and in coculture. Cluster size distributions in chemostats and biofilm reactor effluent were measured. Chlorine susceptibility was assessed for planktonic cultures, attached biofilm, and particles and cells detached from the biofilm. Disinfection tolerance generally increased with a higher percentage of larger cell clusters in the chemostat and detached biofilm. Samples with a lower percentage of large clusters were more easily disinfected. Thus, disinfection tolerance depended on the cluster size distribution rather than sample type for chemostat and detached biofilm. Intact biofilms were more tolerant to chlorine independent of species. Homogenization of samples led to significantly increased susceptibility in all biofilm samples as well as detached clusters for single-species B. cepacia, B. cepacia in coculture, and P. aeruginosa in coculture. The disinfection efficacy was also dependent on species composition; coculture was advantageous to the survival of both species when grown as a biofilm or as clusters detached from biofilm but, surprisingly, resulted in a lower disinfection tolerance when they were grown as a mixed planktonic culture.

Increasing P-stress and viral infection impact lipid remodeling of the picophytoplankter Micromonas pusilla

NASA Astrophysics Data System (ADS)

Maat, D. S.; Bale, N. J.; Hopmans, E. C.; Sinninghe Damsté, J. S.; Schouten, S.; Brussaard, C. P. D.

2015-09-01

The intact polar lipid (IPL) composition of phytoplankton is plastic and dependent on environmental factors. Previous studies have shown that phytoplankton under phosphorus (P)-stress substitute phosphatidylglycerols (PGs) with sulphoquinovosyldiacylglycerols (SQDGs) and digalactosyldiacylglycerols (DGDGs). However, these studies focused merely on P-depletion, while phytoplankton in the natural environment often experience P-limitation whereby the degree of limitation depends on the supply rate of the limiting nutrient. Here we demonstrate a linear increase in SQDG : PG and DGDG : PG ratios with increasing cellular P-stress in the picophotoeukaryote Micromonas pusilla, obtained by P-replete, P-limited (chemostat) and P-starved (no supply of P) culturing conditions. These ratios were not affected by the degree of the P-limiting conditions itself (i.e. 0.97 and 0.32 μmax chemostats), suggesting there is a minimum requirement of PGs for the maintenance of cell growth. Viral infection reduced the increase in SQDG : PG and DGDG : PG ratios in P-starved cells, but the extent did depend on the growth rate of the cultures before infection. The membrane of M. pusilla virus MpV itself was lacking some IPLs compared to the host as, e.g. no monogalactosyldiacylglycerols could be detected. Growth of the phytoplankton cultures under enhanced CO2 concentration did not affect the lipid remodeling results. The present study provides new insights into how the P-related trophic state of an ecosystem as well as viral infection can affect phytoplankton IPL composition, and therefore influence food web dynamics and biogeochemical cycling.

SIMPLAS: A Simulation of Bacterial Plasmid Maintenance.

ERIC Educational Resources Information Center

Dunn, A.; And Others

1988-01-01

This article describes a computer simulation of bacterial physiology during growth in a chemostat. The program was designed to help students to appreciate and understand the related effects of parameters which influence plasmid persistence in bacterial populations. (CW)

Multi-stage microbial system for continuous hydrogen production

DOEpatents

Kosourov, Sergey; Ghirardi, Maria L.; Seibert, Michael

2010-06-08

A method of using sequential chemostat culture vessels to provide continuous H.sub.2 production, in which photosynthetic O.sub.2 evolution and H.sub.2 photoproduction are separated physically into two separate bioreactors, comprising: a) growing a microorganism culture able to continuously generate H.sub.2 by photosynthetically producing cells at about the early-to-late log state in a first photobioreactor operating as a sulfur chemostat under aerobic and/or conditions; b) continuously feeding cells from the first photobioreactor to a second photobioreactor operating under anaerobic conditions and sulfur deprivation conditions resulting from constant uptake of sulfate in the first bioreactor and a low rate of culture flow between the first and second bioreactors, for induction of hydrogenase and H.sub.2 photoproduction to allow for continuous cultivation of the microorganism's cells in the first photobioreactor and constant H.sub.2 production in the second photobioreactor, and c) H.sub.2 gas from the second photobioreactor.

Adsorptive immobilization of a Pseudomonas strain on solid carriers for augmented decolourization in a chemostat bioreactor.

PubMed

Tse, Siu-Wah; Yu, Jian

2003-08-01

Pseudomonas GM3, a highly efficient strain in cleavage of azo bonds of synthetic dyes under anoxic conditions, was immobilized via adsorption on two types of carriers, porous glass beads and solid PVA particles. The cells were cultivated in a nutrient medium, adsorbed on sterile carriers, stabilized as biofilms in repeated batch cultures, and introduced into a chemostat activated sludge reactor for augmented decolourization. The microbial cells were quickly adsorbed and fixed on the PVA surface, compared to a slow and linear immobilization on the glass surface. The porous structure of glass beads provided shelter for the embedded cells, giving a high biomass loading or thick biofilm (13.3 mg VS ml-1 carrier) in comparison with PVA particles (4.8 mg VS ml-1 carrier), but the mass transfer of substrate in the biofilm became a significant limiting factorin the thicker biofilms (effectiveness factor eta = 0.31). The microbial decolourization rate per volume of carriers was 0.15 and 0.17 mg dye ml-1 of glass beads and PVA particles, respectively. In augmented decomposition of a recalcitrant azo dye (60 mg l-1), the immobilized Pseudomonas cells in porous glass beads gave a stable decolourization efficiency (80-81%), but cells fixed on solid PVA particles showed an initial high colour removal of 90% which then declined to a stable removal efficiency of 81%. In both cases, the colour removal efficiency of the chemostat bioreactor was increased from < 10% by an activated sludge to approximately 80% by the augmented system.

Comparing the Chlorine Disinfection of Detached Biofilm Clusters with Those of Sessile Biofilms and Planktonic Cells in Single- and Dual-Species Cultures ▿ †

PubMed Central

Behnke, Sabrina; Parker, Albert E.; Woodall, Dawn; Camper, Anne K.

2011-01-01

Although the detachment of cells from biofilms is of fundamental importance to the dissemination of organisms in both public health and clinical settings, the disinfection efficacies of commonly used biocides on detached biofilm particles have not been investigated. Therefore, the question arises whether cells in detached aggregates can be killed with disinfectant concentrations sufficient to inactivate planktonic cells. Burkholderia cepacia and Pseudomonas aeruginosa were grown in standardized laboratory reactors as single species and in coculture. Cluster size distributions in chemostats and biofilm reactor effluent were measured. Chlorine susceptibility was assessed for planktonic cultures, attached biofilm, and particles and cells detached from the biofilm. Disinfection tolerance generally increased with a higher percentage of larger cell clusters in the chemostat and detached biofilm. Samples with a lower percentage of large clusters were more easily disinfected. Thus, disinfection tolerance depended on the cluster size distribution rather than sample type for chemostat and detached biofilm. Intact biofilms were more tolerant to chlorine independent of species. Homogenization of samples led to significantly increased susceptibility in all biofilm samples as well as detached clusters for single-species B. cepacia, B. cepacia in coculture, and P. aeruginosa in coculture. The disinfection efficacy was also dependent on species composition; coculture was advantageous to the survival of both species when grown as a biofilm or as clusters detached from biofilm but, surprisingly, resulted in a lower disinfection tolerance when they were grown as a mixed planktonic culture. PMID:21856824

Hyperaccumulation of zinc by zinc-depleted Candida utilis grown in chemostat culture.

PubMed

Lawford, H G; Pik, J R; Lawford, G R; Williams, T; Kligerman, A

1980-01-01

The steady-state levels of zinc in Candida utilis yeast grown in continuous culture under conditions of zinc limitations are <1nmol Zn2+/mg dry weight of cells. Unlike carbon-limited cells, zinc-depleted cells from a zinc-limited chemostat possess the capacity to accumulate and store zinc at levels far in excess of the steady-state level of 4 nmol/mg dry biomass observed in carbon-limited chemostat cultures. Zinc uptake is energy-dependent and apparently undirectional since accumulated 65Zn neither exists from preloaded cells nor exchanges with cold Zn2+. The transport system exhibits a high affinity for Zn2+ (Km =.36micrM) with a Vmaxof 2.2 nmol per minute per milligram dry weight of cells. Growth during the period of the uptake assay is responsible for the apparent plateau level of 35 nmol Zn2+/mg dry weight of cells achieved after 20-30 min in the presence of 65Zn at pH 4.5 and 30 degrees C. Inhibition of growth during the uptake assay by cycloheximide results in a biphasic linear pattern of zinc accumulation where the cellular zinc is about 60 nmol/mg dry weight after 1 h. The enhanced level of accumulated zinc is not inhibtory to growth. Zinc-depleted C. utilis contains elevated amounts of polyphosphate and this anionic evidence does not allow discrimination between possible regulation of zinc homestasis either by inhibitions of zinc efflux through control of the membrane carrier or by control of the synthesis of a cytoplasmic zinc-sequestering macromolecule.

Impulsive control of a continuous-culture and flocculation harvest chemostat model

NASA Astrophysics Data System (ADS)

Zhang, Tongqian; Ma, Wanbiao; Meng, Xinzhu

2017-12-01

In this paper, a new mathematical model describing the process of continuous culture and harvest of microalgaes is proposed. By inputting medium and flocculant at two different fixed moments periodically, continuous culture and harvest of microalgaes is implemented. The mathematical analysis is conducted and the whole dynamics of model is investigated by using theory of impulsive differential equations. We find that the model has a microalgaes-extinction periodic solution and it is globally asymptotically stable when some certain threshold value is less than the unit. And the model is permanent when some certain threshold value is larger than the unit. Then, according to the threshold, the control strategies of continuous culture and harvest of microalgaes are discussed. The results show that continuous culture and harvest of microalgaes can be archived by adjusting suitable input time, input amount of medium or flocculant. Finally, some numerical simulations are carried out to verify the control strategy.

In glucose-limited continuous culture the minimum substrate concentration for growth, smin, is crucial in the competition between the enterobacterium Escherichia coli and Chelatobacter heintzii, an environmentally abundant bacterium

PubMed Central

Füchslin, Hans Peter; Schneider, Christian; Egli, Thomas

2012-01-01

The competition for glucose between Escherichia coli ML30, a typical copiotrophic enterobacterium and Chelatobacter heintzii ATCC29600, an environmentally successful strain, was studied in a carbon-limited culture at low dilution rates. First, as a base for modelling, the kinetic parameters μmax and Ks were determined for growth with glucose. For both strains, μmax was determined in batch culture after different precultivation conditions. In the case of C. heintzii, μmax was virtually independent of precultivation conditions. When inoculated into a glucose-excess batch culture medium from a glucose-limited chemostat run at a dilution rate of 0.075 h−1 C. heintzii grew immediately with a μmax of 0.17±0.03 h−1. After five transfers in batch culture, μmax had increased only slightly to 0.18±0.03 h−1. A different pattern was observed in the case of E. coli. Inoculated from a glucose-limited chemostat at D=0.075 h−1 into glucose-excess batch medium E. coli grew only after an acceleration phase of ∼3.5 h with a μmax of 0.52 h−1. After 120 generations and several transfers into fresh medium, μmax had increased to 0.80±0.03 h−1. For long-term adapted chemostat-cultivated cells, a Ks for glucose of 15 μg l−1 for C. heintzii, and of 35 μg l−1 for E. coli, respectively, was determined in 14C-labelled glucose uptake experiments. In competition experiments, the population dynamics of the mixed culture was determined using specific surface antibodies against C. heintzii and a specific 16S rRNA probe for E. coli. C. heintzii outcompeted E. coli in glucose-limited continuous culture at the low dilution rates of 0.05 and 0.075 h−1. Using the determined pure culture parameter values for Ks and μmax, it was only possible to simulate the population dynamics during competition with an extended form of the Monod model, which includes a finite substrate concentration at zero growth rate (smin). The values estimated for smin were dependent on growth rate; at D=0.05 h−1, it was 12.6 and 0 μg l−1 for E. coli and C. heintzii, respectively. To fit the data at D=0.075 h−1, smin for E. coli had to be raised to 34.9 μg l−1 whereas smin for C. heintzii remained zero. The results of the mathematical simulation suggest that it is not so much the higher Ks value, which is responsible for the unsuccessful competition of E. coli at low residual glucose concentration, but rather the existence of a significant smin. PMID:22030672

Continuous microbial cultures maintained by electronically-controlled device

NASA Technical Reports Server (NTRS)

Eisler, W. J., Jr.; Webb, R. B.

1967-01-01

Photocell-controlled instrument maintains microbial culture. It uses commercially available chemostat glassware, provides adequate aeration through bubbling of the culture, maintains the population size and density, continuously records growth rates over small increments of time, and contains a simple, sterilizable nutrient control mechanism.

Concentration-discharge relationships in headwater streams of the Sierra Nevada, California

Treesearch

Carolyn T. Hunsaker; Dale W. Johnson

2017-01-01

We examined streamwater concentration-discharge relationships for eight small, forest watersheds ranging in elevation from 1,485 to 2,465 m in the southern Sierra Nevada. These headwater streams revealed nearly chemostatic behavior by current definitions for K+, Ca...

Multi‐omic profiling ­of EPO‐producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

PubMed Central

Ley, Daniel; Seresht, Ali Kazemi; Engmark, Mikael; Magdenoska, Olivera; Nielsen, Kristian Fog; Kildegaard, Helene Faustrup

2015-01-01

ABSTRACT Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi‐omics approach was applied to study the production of erythropoietin (EPO) in a panel of CHO‐K1 cells under growth‐limited and unlimited conditions in batch and chemostat cultures. Physiological characterization of the EPO‐producing cells included global transcriptome analysis, targeted metabolome analysis, including intracellular pools of glycolytic intermediates, NAD(P)H/NAD(P)+, adenine nucleotide phosphates (ANP), and extracellular concentrations of sugars, organic acids, and amino acids. Potential impact of EPO expression on the protein secretory pathway was assessed at multiple stages using quantitative PCR (qPCR), reverse transcription PCR (qRT‐PCR), Western blots (WB), and global gene expression analysis to assess EPO gene copy numbers, EPO gene expression, intracellular EPO retention, and differentially expressed genes functionally related to secretory protein processing, respectively. We found no evidence supporting the existence of production bottlenecks in energy metabolism (i.e., glycolytic metabolites, NAD(P)H/NAD(P)+ and ANPs) in batch culture or in the secretory protein production pathway (i.e., gene dosage, transcription and post‐translational processing of EPO) in chemostat culture at specific productivities up to 5 pg/cell/day. Time‐course analysis of high‐ and low‐producing clones in chemostat culture revealed rapid adaptation of transcription levels of amino acid catabolic genes in favor of EPO production within nine generations. Interestingly, the adaptation was followed by an increase in specific EPO productivity. Biotechnol. Bioeng. 2015;112: 2373–2387. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:25995028

Influence of oxygen availability on the metabolism and morphology of Yarrowia lipolytica: insights into the impact of glucose levels on dimorphism.

PubMed

Timoumi, Asma; Bideaux, Carine; Guillouet, Stéphane E; Allouche, Yohan; Molina-Jouve, Carole; Fillaudeau, Luc; Gorret, Nathalie

2017-10-01

Dynamic behavior of Yarrowia lipolytica W29 strain under conditions of fluctuating, low, and limited oxygen supply was characterized in batch and glucose-limited chemostat cultures. In batch cultures, transient oscillations between oxygen-rich and -deprived environments induced a slight citric acid accumulation (lower than 29 mg L -1 ). By contrast, no citric acid was detected in continuous fermentations for all stress conditions: full anoxia (zero pO 2 value, 100% N 2 ), limited (zero pO 2 value, 75% of cell needs), and low (pO 2 close to 2%) dissolved oxygen (DO) levels. The macroscopic behavior (kinetic parameters, yields, viability) of Y. lipolytica was not significantly affected by the exposure to DO fluctuations under both modes of culture. Nevertheless, conditions of oxygen limitation resulted in the destabilization of the glucose-limited growth during the continuous cultivations. Morphological responses of Y. lipolytica to DO oscillations were different between batch and chemostat runs. Indeed, a yeast-to-mycelium transition was induced and progressively intensified during the batch fermentations (filamentous subpopulation reaching 74% (v/v)). While, in chemostat bioreactors, the culture consisted mainly of yeast-like cells (mean diameter not exceeding 5.7 μm) with a normal size distribution. During the continuous cultures, growth at low DO concentration did not induce any changes in Y. lipolytica morphology. Dimorphism (up to 80.5% (v/v) of filaments) was only detected under conditions of oxygen limitation in the presence of a residual glucose excess (more than 0.75 g L -1 ). These data suggest an impact of glucose levels on the signaling pathways regulating dimorphic responses in Y. lipolytica.

Acetate scavenging activity in Escherichia coli: interplay of acetyl-CoA synthetase and the PEP-glyoxylate cycle in chemostat cultures.

PubMed

Renilla, Sergio; Bernal, Vicente; Fuhrer, Tobias; Castaño-Cerezo, Sara; Pastor, José M; Iborra, José L; Sauer, Uwe; Cánovas, Manuel

2012-03-01

Impairment of acetate production in Escherichia coli is crucial for the performance of many biotechnological processes. Aerobic production of acetate (or acetate overflow) results from changes in the expression of central metabolism genes. Acetyl-CoA synthetase scavenges extracellular acetate in glucose-limited cultures. Once converted to acetyl-CoA, it can be catabolized by the tricarboxylic acid cycle or the glyoxylate pathway. In this work, we assessed the significance of these pathways on acetate overflow during glucose excess and limitation. Gene expression, enzyme activities, and metabolic fluxes were studied in E. coli knock-out mutants related to the glyoxylate pathway operon and its regulators. The relevance of post-translational regulation by AceK-mediated phosphorylation of isocitrate dehydrogenase for pathway functionality was underlined. In chemostat cultures performed at increasing dilution rates, acetate overflow occurs when growing over a threshold glucose uptake rate. This threshold was not affected in a glyoxylate-pathway-deficient strain (lacking isocitrate lyase, the first enzyme of the pathway), indicating that it is not relevant for acetate overflow. In carbon-limited chemostat cultures, gluconeogenesis (maeB, sfcA, and pck), the glyoxylate operon and, especially, acetyl-CoA synthetase are upregulated. A mutant in acs (encoding acetyl-CoA synthetase) produced acetate at all dilution rates. This work demonstrates that, in E. coli, acetate production occurs at all dilution rates and that overflow is the result of unbalanced synthesis and scavenging activities. The over-expression of acetyl-CoA synthetase by cAMP-CRP-dependent induction limits this phenomenon in cultures consuming glucose at low rate, ensuring the recycling of the acetyl-CoA and acetyl-phosphate pools, although establishing an energy-dissipating substrate cycle.

Effect of culture residence time on substrate uptake and storage by a pure culture of Thiothrix (CT3 strain) under continuous or batch feeding.

PubMed

Valentino, Francesco; Beccari, Mario; Villano, Marianna; Tandoi, Valter; Majone, Mauro

2017-05-25

A pure culture of the filamentous bacterium Thiothrix, strain CT3, was aerobically cultured in a chemostat under continuous acetate feeding at three different culture residence times (RT 6, 12 or 22 d) and the same volumetric organic load rate (OLR 0.12gCOD/L/d). Cells cultured at decreasing RT in the chemostat had an increasing transient response to acetate spikes in batch tests. The maximum specific acetate removal rate increased from 25 to 185mgCOD/gCOD/h, corresponding to a 1.8 to 8.1 fold higher respective steady-state rate in the chemostat. The transient response was mainly due to acetate storage in the form of poly(3-hydroxybutyrate) (PHB), whereas no growth response was observed at any RT. Interestingly, even though the storage rate also decreased as the RT increased, the storage yield increased from 0.41 to 0.50 COD/COD. This finding does not support the traditional view that storage plays a more important role as the transient response increases. The transient response of the steady-state cells was much lower than in cells cultured under periodic feeding (at 6 d RT, from 82 to 247mgCOD/gCOD/h), with the latter cells showing both storage and growth responses. On the other hand, even though steady-state cells had no growth response and their storage rate was also less, steady-state cells showed a higher storage yield than cells cultured under dynamic feeding. This suggests that in Thiothrix strain CT3, the growth response is triggered by periodic feeding, whereas the storage response is a constitutive mechanism, independent from previous acclimation to transient conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions.

PubMed

Henkel, Sebastian G; Ter Beek, Alexander; Steinsiek, Sonja; Stagge, Stefan; Bettenbrock, Katja; de Mattos, M Joost Teixeira; Sauter, Thomas; Sawodny, Oliver; Ederer, Michael

2014-01-01

For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions.

Analysis of Gene Expression in Escherichia coli in Response to Changes of Growth-Limiting Nutrient in Chemostat Cultures

PubMed Central

Hua, Qiang; Yang, Chen; Oshima, Taku; Mori, Hirotada; Shimizu, Kazuyuki

2004-01-01

Studies of steady-state metabolic fluxes in Escherichia coli grown in nutrient-limited chemostat cultures suggest remarkable flux alterations in response to changes of growth-limiting nutrient in the medium (Hua et al., J. Bacteriol. 185:7053-7067, 2003). To elucidate the physiological adaptation of cells to the nutrient condition through the flux change and understand the molecular mechanisms underlying the change in the flux, information on gene expression is of great importance. DNA microarray analysis was performed to investigate the global transcriptional responses of steady-state cells grown in chemostat cultures with limited glucose or ammonia while other environmental conditions and the growth rate were kept constant. In slow-growing cells (specific growth rate of 0.10 h−1), 9.8% of a total of 4,071 genes investigated, especially those involved in amino acid metabolism, central carbon and energy metabolism, transport system and cell envelope, were observed to be differentially expressed between the two nutrient-limited cultures. One important characteristic of E. coli grown under nutrient limitation was its capacity to scavenge carbon or nitrogen from the medium through elevating the expression of the corresponding transport and assimilation genes. The number of differentially expressed genes in faster-growing cells (specific growth rate of 0.55 h−1), however, decreased to below half of that in slow-growing cells, which could be explained by diverse transcriptional responses to the growth rate under different nutrient limitations. Independent of the growth rate, 92 genes were identified as being differentially expressed. Genes tightly related to the culture conditions were highlighted, some of which may be used to characterize nutrient-limited growth. PMID:15066832

Comparison of planktonic and biofilm-associated communities of Clostridium difficile and indigenous gut microbiota in a triple-stage chemostat gut model.

PubMed

Crowther, Grace S; Chilton, Caroline H; Todhunter, Sharie L; Nicholson, Scott; Freeman, Jane; Baines, Simon D; Wilcox, Mark H

2014-08-01

Biofilms are characteristic of some chronic or recurrent infections and this mode of growth tends to reduce treatment efficacy. Clostridium difficile infection (CDI) is associated with a high rate of recurrent symptomatic disease. The presence and behaviour of C. difficile within intestinal biofilms remains largely unexplored, but may factor in recurrent infection. A triple-stage chemostat gut model designed to facilitate the formation of intestinal biofilm was inoculated with a pooled human faecal emulsion. Bacterial populations were allowed to equilibrate before simulated CDI was induced by clindamycin (33.9 mg/L, four times daily, 7 days) and subsequently treated with vancomycin (125 mg/L, four times daily, 7 days). Indigenous gut microbiota, C. difficile total viable counts, spores, cytotoxin and antimicrobial activity in planktonic and biofilm communities were monitored during the 10 week experimental period. Vancomycin successfully treated the initial episode of simulated CDI, but ∼18 days after therapy cessation, recurrent infection occurred. Germination, proliferation and toxin production were evident within planktonic communities in both initial and recurrent CDI. In contrast, sessile C. difficile remained in dormant spore form for the duration of the experiment. The effects of and recovery from clindamycin and vancomycin exposure for sessile populations was delayed compared with responses for planktonic bacteria. Intestinal biofilms provide a potential reservoir for C. difficile spore persistence, possibly facilitating their dispersal into the gut lumen after therapeutic intervention, leading to recurrent infection. Therapeutic options for CDI could have increased efficacy if they are more effective against sessile C. difficile. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Immobilization of infant fecal microbiota and utilization in an in vitro colonic fermentation model.

PubMed

Cinquin, C; Le Blay, G; Fliss, I; Lacroix, C

2004-07-01

Bacteria isolated from infant feces were immobilized in polysaccharide gel beads (2.5% gellan gum, 0.25% xanthan gum) using a two-phase dispersion process. A 52-day continuous culture was carried out in a single-stage chemostat containing precolonized beads and fed with a medium formulated to approximate the composition of infant chyme. Different dilution rates and pH conditions were tested to simulate the proximal (PCS), transverse (TCS), and distal (DCS) colons. Immobilization preserved all nine bacterial groups tested with survival rates between 3 and 56%. After 1 week fermentation, beads were highly colonized with all populations tested (excepted Staphylococcus spp. present in low numbers), which remained stable throughout the 7.5 weeks of fermentation, with variations below 1 log unit. However, free-cell populations in the circulating liquid medium, produced by immobilized cell growth, cell-release activity from gel beads, and free-cell growth, were altered considerably by culture conditions. Compared to the stabilization period, PCS was characterized by a considerable and rapid increase in Bifidobacterium spp. concentrations (7.4 to 9.6 log CFU/mL), whereas Bifidobacterium spp., Lactobacillus spp., and Clostridium spp. concentrations decreased and Staphylococcus spp. and coliforms increased during TCS and DCS. Under pseudo-steady-state conditions, the community structure developed in the chemostat reflected the relative proportions of viable bacterial numbers and metabolites generally encountered in infant feces. This work showed that a complex microbiota such as infant fecal bacteria can be immobilized and used in a continuous in vitro intestinal fermentation model to reproduce the high bacterial concentration and bacterial diversity of the feces inoculum, at least at the genera level, with a high stability during long-term experiment.

Increasing P limitation and viral infection impact lipid remodeling of the picophytoplankter Micromonas pusilla

NASA Astrophysics Data System (ADS)

Maat, Douwe S.; Bale, Nicole J.; Hopmans, Ellen C.; Sinninghe Damsté, Jaap S.; Schouten, Stefan; Brussaard, Corina P. D.

2016-03-01

The intact polar lipid (IPL) composition of phytoplankton is plastic and dependent on environmental factors. Previous studies have shown that phytoplankton under low phosphorus (P) availability substitutes phosphatidylglycerols (PGs) with sulfoquinovosyldiacylglycerols (SQDGs) and digalactosyldiacylglycerols (DGDGs). However, these studies focused merely on P depletion, while phytoplankton in the natural environment often experience P limitation whereby the strength depends on the supply rate of the limiting nutrient. Here we report on the IPL composition of axenic cultures of the picophotoeukaryote Micromonas pusilla under different degrees of P limitation, i.e., P-controlled chemostats at 97 and 32 % of the maximum growth rate, and P starvation (obtained by stopping P supply to these chemostats). P-controlled cultures were also grown at elevated partial carbon dioxide pressure (pCO2) to mimic a future scenario of strengthened vertical stratification in combination with ocean acidification. Additionally, we tested the influence of viral infection for this readily infected phytoplankton host species. Results show that both SQDG : PG and DGDG : PG ratios increased with enhanced P limitation. Lipid composition was, however, not affected by enhanced (750 vs. 370 µatm) pCO2. In the P-starved virally infected cells the increase in SQDG : PG and DGDG : PG ratios was lower, whereby the extent depended on the growth rate of the host cultures before infection. The lipid membrane of the virus MpV-08T itself lacked some IPLs (e.g., monogalactosyldiacylglycerols; MGDGs) in comparison with its host. This study demonstrates that, besides P concentration, also the P supply rate, viral infection and even the history of the P supply rate can affect phytoplankton lipid composition (i.e., the non-phospholipid : phospholipid ratio), with possible consequences for the nutritional quality of phytoplankton.

Transcription of the pst Operon of Clostridium acetobutylicum Is Dependent on Phosphate Concentration and pH

PubMed Central

Fischer, Ralf-Jörg; Oehmcke, Sonja; Meyer, Uta; Mix, Maren; Schwarz, Katrin; Fiedler, Tomas; Bahl, Hubert

2006-01-01

The pst operon of Clostridium acetobutylicum ATCC 824 comprises five genes, pstS, pstC, pstA, pstB, and phoU, and shows a gene architecture identical to that of Escherichia coli. Deduced proteins are predicted to represent a high-affinity phosphate-specific ABC (ATP-binding cassette) transport system (Pst) and a protein homologous to PhoU, a negative phosphate regulon regulator. We analyzed the expression patterns of the pst operon in Pi-limited chemostat cultures during acid production at pH 5.8 or solvent production at pH 4.5 and in response to Pi pulses. Specific mRNA transcripts were found only when external Pi concentrations had dropped below 0.2 mM. Two specific transcripts were detected, a 4.7-kb polycistronic mRNA spanning the whole operon and a quantitatively dominating 1.2-kb mRNA representing the first gene, pstS. The mRNA levels clearly differed depending on the external pH. The amounts of the full-length mRNA detected were about two times higher at pH 5.8 than at pH 4.5. The level of pstS mRNA increased by a factor of at least 8 at pH 5.8 compared to pH 4.5 results. Primer extension experiments revealed only one putative transcription start point 80 nucleotides upstream of pstS. Thus, additional regulatory sites are proposed in the promoter region, integrating two different extracellular signals, namely, depletion of inorganic phosphate and the pH of the environment. After phosphate pulses were applied to a phosphate-limited chemostat we observed faster phosphate consumption at pH 5.8 than at pH 4.5, although higher optical densities were recorded at pH 4.5. PMID:16855236

METHANOGENESIS AND SULFATE REDUCTION IN CHEMOSTATS: II. MODEL DEVELOPMENT AND VERIFICATION

EPA Science Inventory

A comprehensive dynamic model is presented that simulates methanogenesis and sulfate reduction in a continuously stirred tank reactor (CSTR). This model incorporates the complex chemistry of anaerobic systems. A salient feature of the model is its ability to predict the effluent ...

Anaerobic Biodegradation of Soybean Biodiesel and Diesel Blends under Methanogenic Conditions

EPA Science Inventory

Biotransformation of soybean biodiesel and the inhibitory effect of petrodiesel were studied under methanogenic conditions. Biodiesel removal efficiency of more than 95% was achieved in a chemostat with influent biodiesel concentrations up to 2.45 g/L. The kinetics of anaerobic...

Long period grating-based fiber-optic PH sensor for ocean monitoring

NASA Astrophysics Data System (ADS)

Wang, Ke; Klimov, Denis; Kolber, Zbigniew

2007-09-01

A fiber-optic PH sensor is developed based-on the long period grating (LPG). The LPG is fabricated by using CO II laser with a point-by-point technique. Then the grating portion is coated with PH sensitive hydrogel. The hydrogel, made of PVA/PAA, swells its volume in response to the PH change in the surrounding environment and results in a change in the refractive index. As a result, the LPG can response to the refractive index change in the coating by shifting its wavelength. Therefore, change in refractive index can be measured by tracking the wavelength shift using an optical spectrum analyzer (OSA). In this research, the LPG is dip-coated by the hydrogel. A chemostat is designed to simulate the marine environment. The PH in the chemostat is varied by controlling the CO II concentration in the sea water. A PH resolution 0.046/nm using the OSA has been obtained. This sensor is designed to monitor the sea water PH change in a long term basis.

A novel directly coupled gradostat

NASA Technical Reports Server (NTRS)

Wimpenny, J. W.; Earnshaw, R. G.; Gest, H.; Hayes, J. M.; Favinger, J. L.

1992-01-01

The original bidirectional compound chemostat (gradostat) described by Lovitt and Wimpenny has been simplified by making a more compact apparatus in which chemical gradients are established by diffusion between adjacent culture chambers. The experimental model (diffusion coupled (DC) gradostat) consisted of five chambers whose contents could be agitated by turbines rotating in the horizontal plane on a common shaft. Two biological experiments were designed to reveal the value of the DC gradostat. A methylotroph (Methylophilus methylotrophus) grown in a methanol gradient showed expected changes in cell viability as a function of position in the five vessel array. Cells of two species of photosynthetic bacteria (Rhodobacter capsulata and Rhodopseudomonas marina/agilis) with different salt sensitivities could be mixed and subsequently separated by the DC gradostat operating with a NaCl gradient of 0-3% w/v.

Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

PubMed Central

2012-01-01

Background Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations. Results Starting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways. Conclusions The work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory. PMID:23043429

Efficiencies of Bio-electrocatalytic Production of Hydrogen from Lactate Using Shewanella oneidensis MR-1

USDA-ARS?s Scientific Manuscript database

Shewanella oneidensis MR-1 was grown in a chemostatic, continuously-fed bioelectrochemical cell under slightly aerated conditions. The start-up phase was controlled potentiostatically (0.4 V vs. SHE). When a stable performance was achieved, the reactor was switched to bio-electrocatalytic producti...

Multi-stage Continuous Culture Fermentation of Glucose-Xylose Mixtures to Fuel Ethanol using Genetically Engineered Saccharomyces cerevisiae 424A

EPA Science Inventory

Multi-stage continuous (chemostat) culture fermentation (MCCF) with variable fermentor volumes was carried out to study utilizing glucose and xylose for ethanol production by means of mixed sugar fermentation (MSF). Variable fermentor volumes were used to enable enhanced sugar u...

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius

DOE PAGES

Lee, Brady D.; Apel, William A.; DeVeaux, Linda C.; ...

2017-08-03

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in this paper in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grewmore » while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Finally, microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.« less

Biotransformation of d-Limonene to (+) trans-Carveol by Toluene-Grown Rhodococcus opacus PWD4 Cells

PubMed Central

Duetz, Wouter A.; Fjällman, Ann H. M.; Ren, Shuyu; Jourdat, Catherine; Witholt, Bernard

2001-01-01

The toluene-degrading strain Rhodococcus opacus PWD4 was found to hydroxylate d-limonene exclusively in the 6-position, yielding enantiomerically pure (+) trans-carveol and traces of (+) carvone. This biotransformation was studied using cells cultivated in chemostat culture with toluene as a carbon and energy source. The maximal specific activity of (+) trans-carveol formation was 14.7 U (g of cells [dry weight])−1, and the final yield was 94 to 97%. Toluene was found to be a strong competitive inhibitor of the d-limonene conversion. Glucose-grown cells did not form any trans-carveol from d-limonene. These results suggest that one of the enzymes involved in toluene degradation is responsible for this allylic monohydroxylation. Another toluene degrader (Rhodococcus globerulus PWD8) had a lower specific activity but was found to oxidize most of the formed trans-carveol to (+) carvone, allowing for the biocatalytic production of this flavor compound. PMID:11375201

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Brady D.; Apel, William A.; DeVeaux, Linda C.

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in this paper in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grewmore » while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Finally, microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.« less

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

USDA-ARS?s Scientific Manuscript database

Bacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host-derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, in...

Light intensity as major factor to maximize biomass and lipid productivity of Ettlia sp. in CO2-controlled photoautotrophic chemostat.

PubMed

Seo, Seong-Hyun; Ha, Ji-San; Yoo, Chan; Srivastava, Ankita; Ahn, Chi-Yong; Cho, Dae-Hyun; La, Hyun-Joon; Han, Myung-Soo; Oh, Hee-Mock

2017-11-01

The optimal culture conditions are critical factors for high microalgal biomass and lipid productivity. To optimize the photoautotrophic culture conditions, combination of the pH (regulated by CO 2 supply), dilution rate, and light intensity was systematically investigated for Ettlia sp. YC001 cultivation in a chemostat during 143days. The biomass productivity increased with the increase in dilution rate and light intensity, but decreased with increasing pH. The average lipid content was 19.8% and statistically non-variable among the tested conditions. The highest biomass and lipid productivities were 1.48gL -1 d -1 and 291.4mgL -1 d -1 with a pH of 6.5, dilution rate of 0.78d -1 , and light intensity of 1500μmolphotonsm -2 s -1 . With a sufficient supply of CO 2 and nutrients, the light intensity was the main determinant of the photosynthetic rate. Therefore, the surface-to-volume ratio of a photobioreactor should enable efficient light distribution to enhance microalgal growth. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats.

PubMed

Marozava, Sviatlana; Vargas-López, Raquel; Tian, Ye; Merl-Pham, Juliane; Braster, Martin; Meckenstock, Rainer U; Smidt, Hauke; Röling, Wilfred F M; Westerhoff, Hans V

2018-06-19

Desulfitobacterium hafniense Y51 has been widely used in investigations of perchloroethylene (PCE) biodegradation, but limited information exists on its other physiological capabilities. We investigated how D. hafniense Y51 confronts the debilitating limitations of not having enough electron donor (lactate), or electron acceptor (fumarate) during cultivation in chemostats. The residual concentrations of the substrates supplied in excess were much lower than expected. Transcriptomics, proteomics, and fluxomics were integrated to investigate how this phenomenon was regulated. Through diverse regulation at both transcriptional and translational levels, strain Y51 turned to fermenting the excess lactate and disproportionating the excess fumarate under fumarate- and lactate-limiting conditions, respectively. Genes and proteins related to the utilization of a variety of alternative electron donors and acceptors absent from the medium were induced, apparently involving the Wood-Ljungdahl pathway. Through this metabolic flexibility, D. hafniense Y51 may be able to switch between different metabolic capabilities under limiting conditions. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Adapting High-Resolution Respirometry to Glucose-Limited Steady State Mycelium of the Filamentous Fungus Penicillium ochrochloron: Method Development and Standardisation

PubMed Central

Schinagl, Christoph W.; Vrabl, Pamela; Burgstaller, Wolfgang

2016-01-01

Fungal electron transport systems (ETS) are branched, involving alternative NADH dehydrogenases and an alternative terminal oxidase. These alternative respiratory enzymes were reported to play a role in pathogenesis, production of antibiotics and excretion of organic acids. The activity of these alternative respiratory enzymes strongly depends on environmental conditions. Functional analysis of fungal ETS under highly standardised conditions for cultivation, sample processing and respirometric assay are still lacking. We developed a highly standardised protocol to explore in vivo the ETS—and in particular the alternative oxidase—in Penicillium ochrochloron. This included cultivation in glucose-limited chemostat (to achieve a defined and reproducible physiological state), direct transfer without any manipulation of a broth sample to the respirometer (to maintain the physiological state in the respirometer as close as possible to that in the chemostat), and high-resolution respirometry (small sample volume and high measuring accuracy). This protocol was aimed at avoiding any changes in the physiological phenotype due to the high phenotypic plasticity of filamentous fungi. A stable oxygen consumption (< 5% change in 20 minutes) was only possible with glucose limited chemostat mycelium and a direct transfer of a broth sample into the respirometer. Steady state respiration was 29% below its maximum respiratory capacity. Additionally to a rotenone-sensitive complex I and most probably a functioning complex III, the ETS of P. ochrochloron also contained a cyanide-sensitive terminal oxidase (complex IV). Activity of alternative oxidase was present constitutively. The degree of inhibition strongly depended on the sequence of inhibitor addition. This suggested, as postulated for plants, that the alternative terminal oxidase was in dynamic equilibrium with complex IV—independent of the rate of electron flux. This means that the onset of activity does not depend on a complete saturation or inhibition of the cytochrome pathway. PMID:26771937

Selective sweeps in growing microbial colonies

NASA Astrophysics Data System (ADS)

Korolev, Kirill S.; Müller, Melanie J. I.; Karahan, Nilay; Murray, Andrew W.; Hallatschek, Oskar; Nelson, David R.

2012-04-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.

Building a Morbidostat: An automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition

PubMed Central

Toprak, Erdal; Veres, Adrian; Yildiz, Sadik; Pedraza, Juan M.; Chait, Remy; Paulsson, Johan; Kishony, Roy

2013-01-01

We present a protocol for building and operating an automated fluidic system for continuous culture that we call the “morbidostat”. The morbidostat is used to follow evolution of microbial drug resistance in real time. Instead of exposing bacteria to predetermined drug environments, the morbidostat constantly measures the growth rates of evolving microbial populations and dynamically adjusts drug concentrations inside culture vials in order to maintain a constant drug induced inhibition. The growth rate measurements are done using an optical detection system that is based on measuring the intensity of back-scattered light from bacterial cells suspended in the liquid culture. The morbidostat can additionally be used as a chemostat or a turbidostat. The whole system can be built from readily available components within two to three weeks, by biologists with some electronics experience or engineers familiar with basic microbiology. PMID:23429717

Hxt-carrier-mediated glucose efflux upon exposure of Saccharomyces cerevisiae to excess maltose.

PubMed

Jansen, Mickel L A; De Winde, Johannes H; Pronk, Jack T

2002-09-01

When wild-type Saccharomyces cerevisiae strains pregrown in maltose-limited chemostat cultures were exposed to excess maltose, release of glucose into the external medium was observed. Control experiments confirmed that glucose release was not caused by cell lysis or extracellular maltose hydrolysis. To test the hypothesis that glucose efflux involved plasma membrane glucose transporters, experiments were performed with an S. cerevisiae strain in which all members of the hexose transporter (HXT) gene family had been eliminated and with an isogenic reference strain. Glucose efflux was virtually eliminated in the hexose-transport-deficient strain. This constitutes experimental proof that Hxt transporters facilitate export of glucose from S. cerevisiae cells. After exposure of the hexose-transport-deficient strain to excess maltose, an increase in the intracellular glucose level was observed, while the concentrations of glucose 6-phosphate and ATP remained relatively low. These results demonstrate that glucose efflux can occur as a result of uncoordinated expression of the initial steps of maltose metabolism and the subsequent reactions in glucose dissimilation. This is a relevant phenomenon for selection of maltose-constitutive strains for baking and brewing.

Hxt-Carrier-Mediated Glucose Efflux upon Exposure of Saccharomyces cerevisiae to Excess Maltose

PubMed Central

Jansen, Mickel L. A.; De Winde, Johannes H.; Pronk, Jack T.

2002-01-01

When wild-type Saccharomyces cerevisiae strains pregrown in maltose-limited chemostat cultures were exposed to excess maltose, release of glucose into the external medium was observed. Control experiments confirmed that glucose release was not caused by cell lysis or extracellular maltose hydrolysis. To test the hypothesis that glucose efflux involved plasma membrane glucose transporters, experiments were performed with an S. cerevisiae strain in which all members of the hexose transporter (HXT) gene family had been eliminated and with an isogenic reference strain. Glucose efflux was virtually eliminated in the hexose-transport-deficient strain. This constitutes experimental proof that Hxt transporters facilitate export of glucose from S. cerevisiae cells. After exposure of the hexose-transport-deficient strain to excess maltose, an increase in the intracellular glucose level was observed, while the concentrations of glucose 6-phosphate and ATP remained relatively low. These results demonstrate that glucose efflux can occur as a result of uncoordinated expression of the initial steps of maltose metabolism and the subsequent reactions in glucose dissimilation. This is a relevant phenomenon for selection of maltose-constitutive strains for baking and brewing. PMID:12200274

Recalibrating the concentration of Precambrian seawater sulfate

NASA Astrophysics Data System (ADS)

Johnston, D. T.; Bradley, A. S.; Hoarfrost, A.; Girguis, P. R.

2010-12-01

The isotopic offset between sulfate sulfur and sulfide sulfur (δ34Ssulfate-sulfide) is widely used in the Precambrian as a paleo-indicator of seawater sulfate concentrations. Popularized by experimental work proposing an increase in seawater sulfate at the Archean - Proterozoic boundary, the concept of using a calibrated physiological process (dissimilatory sulfate reduction) to extract environmental information holds the potential to unlock numerous geological questions. To that end, the interpretability of sulfur isotope records relies on the degree to which strict quantitative constraints have been placed on the relationship between sulfate concentrations and sulfate reducing bacteria. Our work serves to extend those constraints. Here we present data from a series of replicate quasi-chemostat microbial reactors, inoculated with marine sediment from Monterey Bay and incubated with artificial seawater ([SO42-]< 5 mM). Our experimental design continuously removes sulfide and allows for systematic tracking of the dependence of δ34Ssulfate-sulfide on seawater sulfate concentration. In addition to expanding the existing δ34S context, we target high-precision multiple sulfur isotope data, which allows for a greater interpretability of both the overall result and its mapping onto environmental records. Further, we use natural abundance and δ18O spiked water within our experiments to assay rates of cellular re-oxidation (within the sulfate reduction pathway) and to constrain natural δ18O effects within these systems. Finally, we use modern molecular biological techniques to track community structure as a function of time and environmental conditions. Together, these data provide an integrated metric with which to interpret complex natural sulfur isotope records.

Control of Nonlinear Systems

DTIC Science & Technology

2004-01-01

variables reinforce each other (positive feedback) as well as certain more general systems in which each pair of variables may affect each other in...characteristics, and applied to presented small-gain theorems guaranteeing the lack of oscillatory or more complicated behavior in a large class of Lotka ... Volterra systems with predator-prey interactions as well as chemostats, which describe the interaction between microbial species which are competing

¹³C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect.

PubMed

Kajihata, Shuichi; Matsuda, Fumio; Yoshimi, Mika; Hayakawa, Kenshi; Furusawa, Chikara; Kanda, Akihisa; Shimizu, Hiroshi

2015-08-01

Saccharomyces cerevisiae shows a Crabtree effect that produces ethanol in a high glucose concentration even under fully aerobic condition. For efficient production of cake yeast or compressed yeast for baking, ethanol by-production is not desired since glucose limited chemostat or fed-batch cultivations are performed to suppress the Crabtree effect. In this study, the (13)C-based metabolic flux analysis ((13)C-MFA) was performed for the S288C derived S. cerevisiae strain to characterize a metabolic state under the reduced Crabtree effect. S. cerevisiae cells were cultured at a low dilution rate (0.1 h(-1)) under the glucose-limited chemostat condition. The estimated metabolic flux distribution showed that the acetyl-CoA in mitochondria was mainly produced from pyruvate by pyruvate dehydrogenase (PDH) reaction and that the level of the metabolic flux through the pentose phosphate pathway was much higher than that of the Embden-Meyerhof-Parnas pathway, which contributes to high biomass yield at low dilution rate by supplying NADPH required for cell growth. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Optimisation of culture conditions with respect to biotin requirement for the production of recombinant avidin in Pichia pastoris.

PubMed

Jungo, Carmen; Urfer, Julien; Zocchi, Andrea; Marison, Ian; von Stockar, Urs

2007-01-20

Due to its very high affinity to biotin, avidin is one of the most widely exploited proteins in modern biotechnological and biomedical applications. Since biotin is an essential vitamin for the growth of many microorganisms, we examined the effect of biotin deficiency on growth for a recombinant Pichia pastoris strain expressing and secreting a recombinant glycosylated avidin. The results showed that biotin deficiency lowers growth rate and biomass yield for P. pastoris. Substitution of biotin in the medium by the two structurally unrelated compounds, aspartic acid and oleic acid, which do not bind to recombinant avidin was analyzed quantitatively. These two compounds had a growth promoting effect in biotin-deficient medium, but did not replace biotin completely. Indeed, in chemostat culture, wash-out occurred after about six liquid residence times and recombinant avidin productivity was lowered. However, addition of low amounts of biotin (20 microg L(-1) of biotin for a cell density of 8 g L(-1)) resulted in stable chemostat cultures on methanol with the production of recombinant biotin-free avidin. The specific avidin production rate was 22 microg g(-1) h(-1) at a dilution rate of 0.06 h(-1).

Sulfur formation by steady-state continuous cultures of a sulfoxidizing consortium and Thiobacillus thioparus ATCC 23645.

PubMed

Alcántara, S; Velasco, A; Revah, S

2004-10-01

The elemental sulfur formation by the partial oxidation of thiosulfate by both a sulfoxidizing consortium and by Thiobacillus thioparus ATCC 23645 was studied under aerobic conditions in chemostat. Steady state was attained with essentially total conversion to sulfate when the dissolved oxygen concentration was 5 mgO2 l(-1) and below a dilution rate (D) of 3.0 d(-1)for the consortium and 0.9 d(-1) for T thioparus. The consortium formed elemental sulfur in steady state under oxygen limitation. Fifty percent of the theoretical elemental sulfur yield was obtained with a dissolved oxygen concentration of 0.2 mgO2 l(-1). Growth of T thioparus was negatively affected with a concentration below 1.9 mgO2 l(-1). Consortium yield from batch cultures was 2.1 g(-1) (protein) mol(-1) (thiosulfate), which was comparable with the values obtained in the chemostat at dilution rates of 0.4 d(-1) and 1.2 d(-1). The consortium showed a maximum degradation rate of 0.105 g(thiosulfate) g(-1) (protein) min(-1) and a saturation rate for S2O3(2-) of 1.9 mM.

Two tales of legacy effects on stream nutrient behaviour

NASA Astrophysics Data System (ADS)

Bieroza, M.; Heathwaite, A. L.

2017-12-01

Intensive agriculture has led to large-scale land use conversion, shortening of flow pathways and increased loads of nutrients in streams. This legacy results in gradual build-up of nutrients in agricultural catchments: in soil for phosphorus (biogeochemical legacy) and in the unsaturated zone for nitrate (hydrologic legacy), controlling the water quality in the long-term. Here we investigate these effects on phosphorus and nitrate stream concentrations using high-frequency (10-5 - 100 Hz) sampling with in situ wet-chemistry analysers and optical sensors. Based on our 5 year study, we observe that storm flow responses differ for both nutrients: phosphorus shows rapid increases (up to 3 orders of magnitude) in concentrations with stream flow, whereas nitrate shows both dilution and concentration effects with increasing flow. However, the range of nitrate concentrations change is narrow (up to 2 times the mean) and reflects chemostatic behaviour. We link these nutrient responses with their dominant sources and flow pathways in the catchment. Nitrate from agriculture (with the peak loading in 1983) is stored in the unsaturated zone of the Penrith Sandstone, which can reach up to 70 m depth. Thus nitrate legacy is related to a hydrologic time lag with long travel times in the unsaturated zone. Phosphorus is mainly sorbed to soil particles, therefore it is mobilised rapidly during rainfall events (biogeochemical legacy). The phosphorus stream response will however depend on how well connected is the stream to the catchment sources (driven by soil moisture distribution) and biogeochemical activity (driven by temperature), leading to both chemostatic and non-chemostatic responses, alternating on a storm-to-storm and seasonal basis. Our results also show that transient within-channel storage is playing an important role in delivery of phosphorus, providing an additional time lag component. These results show, that consistent agricultural legacy in the catchment (high historical loads of nutrients) has different effects on nutrients stream responses, depending on their dominant sources and pathways. Both types of time lags, biogeochemical for phosphorus and hydrologic for nitrate, need to be taken into account when designing and evaluating the effectiveness of the agri-environmental mitigation measures.

Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

PubMed Central

Airoldi, Edoardo M.; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David

2016-01-01

Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR-regulated permease genes GAP1, MEP2, DAL5, PUT4, and DIP5. Our results reveal novel aspects of nitrogen-regulated gene expression and highlight the need for a quantitative approach to study how the cell coordinates protein translation and nitrogen assimilation to optimize cell growth in different environments. PMID:26941329

Turnover of cyclic 2,3-diphosphoglycerate in Methanobacterium thermoautotrophicum. Phosphate flux in P1- and H2-limited chemostat cultures.

PubMed

Krueger, R D; Campbell, J W; Fahrney, D E

1986-09-15

The archaebacterium Methanobacterium thermoautotrophicum was grown at 65 degrees C in H2- and Pi-limited chemostat cultures at dilution rates corresponding to 3- and 4-h doubling times, respectively. Under these conditions the steady state concentration of cyclic 2,3-diphosphoglycerate was 44 mM in the H2-limited cells and 13 mM in the cells grown under Pi limitation. Flux of Pi into the cyclic pyrophosphate pool was estimated by two 32P-labeling procedures: approach to isotopic equilibrium and replacement of prelabeled cyclic diphosphoglycerate with unlabeled compound. The results unequivocally demonstrate turnover of the phosphoryl groups; either both phosphoryl groups of the cyclic pyrophosphate leave together or the second leaves at a faster rate. The half-life of the rate-determining step for loss of the phosphoryl groups was approximately equal to the culture doubling time. The Pi flowing into the cyclic diphosphoglycerate pool accounted for 19% of the total Pi flux into Pi-limited cells and 43% of the total for H2-limited cells. The high phosphate flux through the large cyclic diphosphoglycerate pool suggests that this molecule plays an important role in the phosphorus metabolism of this methanogen.

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast

PubMed Central

Brickwedde, Anja; van den Broek, Marcel; Geertman, Jan-Maarten A.; Magalhães, Frederico; Kuijpers, Niels G. A.; Gibson, Brian; Pronk, Jack T.; Daran, Jean-Marc G.

2017-01-01

The lager brewing yeast Saccharomyces pastorianus, an interspecies hybrid of S. eubayanus and S. cerevisiae, ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion (“attenuation”) of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains. PMID:28943864

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast.

PubMed

Brickwedde, Anja; van den Broek, Marcel; Geertman, Jan-Maarten A; Magalhães, Frederico; Kuijpers, Niels G A; Gibson, Brian; Pronk, Jack T; Daran, Jean-Marc G

2017-01-01

The lager brewing yeast Saccharomyces pastorianus , an interspecies hybrid of S. eubayanus and S. cerevisiae , ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion ("attenuation") of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14 C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains.

Environmental stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations.

PubMed

Lieder, Sarah; Jahn, Michael; Koepff, Joachim; Müller, Susann; Takors, Ralf

2016-01-01

Cellular response to different types of stress is the hallmark of the cell's strategy for survival. How organisms adjust their cell cycle dynamics to compensate for changes in environmental conditions is an important unanswered question in bacterial physiology. A cell using binary fission for reproduction passes through three stages during its cell cycle: a stage from cell birth to initiation of replication, a DNA replication phase and a period of cell division. We present a detailed analysis of durations of cell cycle phases, investigating their dynamics under environmental stress conditions. Applying continuous steady state cultivations (chemostats), the DNA content of a Pseudomonas putida KT2440 population was quantified with flow cytometry at distinct growth rates. Data-driven modeling revealed that under stress conditions, such as oxygen deprivation, solvent exposure and decreased iron availability, DNA replication was accelerated correlated to the severity of the imposed stress (up to 1.9-fold). Cells maintained constant growth rates by balancing the shortened replication phase with extended cell cycle phases before and after replication. Transcriptome data underpin the transcriptional upregulation of crucial genes of the replication machinery. Hence adaption of DNA replication speed appears to be an important strategy to withstand environmental stress. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

PubMed

Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

2016-02-01

The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future.

pH regulation of recombinant glucoamylase production in Fusarium venenatum JeRS 325, a transformant with a Fusarium oxysporum alkaline (trypsin-like) protease promoter.

PubMed

Wiebe, M G; Robson, G D; Shuster, J R; Trinci, A P

1999-08-05

Fusarium venenatum (formerly Fusarium graminearum) JeRS 325 produces heterologous glucoamylase (GAM) under the regulation of a Fusarium oxysporum alkaline (trypsin-like) protease promoter. The glucoamylase gene was used as a reporter gene to study the effects of ammonium and pH on GAM production under the control of the alkaline protease promoter. Between pH 4.0 and 5.8, GAM production in glucose-limited chemostat cultures of JeRS 325 grown at a dilution rate of 0.10 h-1 (doubling time, 6.9 h) on (NH4)2SO4 medium increased in a linear manner with increase in pH. However, at pH 4.0 and below GAM production was almost completely repressed in glucose-limited chemostat cultures grown on (NH4)2SO4 or NaNO3 medium. Thus GAM production in JeRS 325 is regulated by culture pH, not by the nature of the nitrogen source in the medium. The difficulty of using unbuffered medium when investigating putative ammonium repression is also shown. The study demonstrates the potential for use of the alkaline protease promoter in F. graminearum for the production of recombinant proteins in a pH dependent man ner. Copyright 1999 John Wiley & Sons, Inc.

EFFECT OF TEMPERATURE ON THE COMPOSITION OF FATTY ACIDS IN ESCHERICHIA COLI

PubMed Central

Marr, Allen G.; Ingraham, John L.

1962-01-01

Marr, Allen G. (University of California, Davis) and John L. Ingraham. Effect of temperature on composition of fatty acids in Escherichia coli. J. Bacteriol. 84:1260–1267. 1962.—Variations in the temperature of growth and in the composition of the medium alter the proportions of individual fatty acids in the lipids of Escherichia coli. As the temperature of growth is lowered, the proportion of unsaturated fatty acids (hexadecenoic and octadecenoic acids) increases. The increase in content of unsaturated acids with a decrease in temperature of growth occurs in both minimal and complex media. Cells harvested in the stationary phase contained large amounts of cyclopropane fatty acids (methylenehexadecanoic and methylene octadecanoic acids) in comparison with cells harvested during exponential growth. Cells grown in a chemostat, limited by the concentration of ammonium salts, show a much higher content of saturated fatty acids (principally palmitic acid) than do cells harvested from an exponentially-growing batch culture in the same medium. Cells grown in a chemostat, limited by the concentration of glucose, show a slightly higher content of unsaturated fatty acids than cells from the corresponding batch culture. The results do not indicate a direct relation between fatty acid composition and minimal growth temperature. PMID:16561982

Continuous Microfluidics (Ecology-on-a-Chip) Experiments for Long Term Observation of Bacteria at Liquid-Liquid Interfaces

NASA Astrophysics Data System (ADS)

Miranda, Michael; White, Andrew; Jalali, Maryam; Sheng, Jian

2017-11-01

A microfluidic bioassay incorporating a peristaltic pump and chemostat capable of continuously culturing a bacterial suspension through a microchannel for an extended period of time relevant to ecological processes is presented. A single crude oil droplet is dispensed on-chip and subsequently pinned to the top and bottom surfaces of the microchannel to establish a vertical curved oil-water interface to observe bacteria without boundary interference. The accumulation of extracellular polymeric substances (EPS), microbial film formation, and aggregation is provided by DIC microscopy with an EMCCD camera at an interval of 30 sec. Cell-interface interactions such as cell translational and angular motilities as well as encountering, attachment, detachment to the interface are obtained by a high speed camera at 1000 fps with a sampling interval of 10 min. Experiments on Pseudomonas sp. (P62) and isolated EPS suspensions from Sagitulla Stelleta and Roseobacter show rapid formation of bacterial aggregates including EPS streamers stretching tens of drop diameters long. These results provide crucial insights into environmentally relevant processes such as the initiation of marine oil snow, an alternative mode of biodegradation to conventional bioconsumption. Funded by GoMRI, NSF, ARO.

Perennial flow through convergent hillslopes explains chemodynamic solute behavior in a shale headwater catchment

NASA Astrophysics Data System (ADS)

Herndon, E.; Steinhoefel, G.; Dere, A. L. D.; Sullivan, P. L.

2017-12-01

Streams experience changing hydrologic connectivity to heterogeneous water sources under different flow regimes. It remains unclear how seasonal flow paths link these different sources and regulate concentration-discharge behavior. Previous research at the Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in central Pennsylvania, USA identified chemostatic solutes (e.g., K, Mg, Na, Cl) whose concentrations varied little across a wide range of discharge values and chemodynamic solutes (e.g., Fe and Mn) whose concentrations decreased sharply with increasing stream discharge. To elucidate inputs to the stream when concentrations of chemodynamic solutes were high, we investigated stream water and shallow groundwater (< 4 m) chemistry at the SSHCZO in early autumn when discharge was negligible. The stream consisted of isolated puddles that were chemically variable along the length of the channel but similar to underlying shallow groundwater. Chemodynamic solute concentrations in the stream and groundwater were high in the upper catchment but decreased by an order of magnitude towards the outlet. In contrast, chemostatic solute concentrations varied little. Groundwater was minimally connected to the stream in an area of upwelling near the stream headwaters; however, the water table remained over a meter below the stream bed along the rest of the channel. We conclude that well water sampled from the upper catchment is young, shallow interflow that upwells to generate metal-rich stream headwaters during the dry season. High concentrations of chemodynamic solutes measured during low discharge occur when metal-rich headwaters are flushed to the catchment outlet during periodic rain events. Interflow during the dry season originates from water that infiltrates through organic-rich swales; thus, metals in the stream at low flow are ultimately derived from convergent hillslopes where biological processes have concentrated chemodynamic elements. We infer that chemodynamic solutes are diluted at high discharge due to increased flow through planar hillslopes and inputs from regional groundwater that rises to enter the stream. This study highlights how spatially heterogeneous biogeochemistry and seasonally variable flow paths regulate concentration-discharge behavior within catchments.

Reductive Dechlorination of Carbon Tetrachloride by Tetrachloroethene and Trichloroethene Respiring Anaerobic Mixed Cultures

NASA Astrophysics Data System (ADS)

Vickstrom, K. E.; Azizian, M.; Semprini, L.

2015-12-01

Carbon tetrachloride (CT) is a toxic and recalcitrant groundwater contaminant with the potential to form a broad range of transformation products. Of the possible biochemical pathways through which CT can be degraded, reductive dehalogenation to less chlorinated compounds and mineralization to carbon dioxide (CO2) appear to be the most frequently utilized pathways by anaerobic organisms. Results will be presented from batch experiments of CT degradation by the Evanite (EV), Victoria Strain (VS) and Point Mugu (PM) anaerobic dechlorinating cultures. The cultures are grown in chemostats and are capable of transforming tetrachloroethene (PCE) or trichloroethene (TCE) to ethene by halorespiration via reductive dehalogenase enzymes. For the batch CT transformation tests, the cells along with supernatant were harvested from chemostats fed PCE or TCE, but never CT. The batch reactors were initially fed 0.0085 mM CT and an excess of formate (EV and VS) or lactate (PM) as electron donor. Transformation of CT was 100% with about 20% converted to chloroform (CF) and undetected products. Multiple additions of CT showed a slowing of pseudo first-order CT transformation rates across all cultures. Batch reactors were then established and fed 0.085 mM CT with an excess of electron donor in order to better quantify the reductive pathway. CT was transformed to CF and dichloromethane (DCM), with trace amounts of chloromethane (CM) detected. Between 60-90% of the mass added to the system was accounted for, showing that the majority of the carbon tetrachloride present is being reductively dehalogenated. Results from batch reactors that were poisoned using sodium azide, and from reactors not provided electron donor will be presented to distinguish between biotic and abiotic reactions. Furthermore, results from reactors prepared with acetylene (a potent, reversible inhibitor of reductive dehalogenases (1)) will be presented as a means of identifying the enzymes involved in the transformation of CT. The results clearly demonstrate that reductive dechlorination of CT can be promoted by anaerobic cultures not previously acclimated to CT. 1. G. Pon, M. R. Hyman, L. Semprini, Environ. Sci. Technol. 37, 3181-3188 (2003).

Characterization of serological cross-reactivity between polysaccharide antigens of Streptococcus mutans serotypes c and d.

PubMed

Grossi, S; Prakobphol, A; Linzer, R; Campbell, L K; Knox, K W

1983-03-01

Immunological assays with antisera prepared against purified Streptococcus mutans serotype c polysaccharide demonstrated that a cross-reacting determinant on c polysaccharide reacted with the wall-associated rhamnose-glucose polysaccharide from S. mutans serotype d. Studies with 60 antisera prepared against chemostat cultures of S. mutans Ingbritt (c) demonstrated that the rhamnose-glucose polysaccharide cross-reactive determinant was consistently expressed on c antigen under a variety of growth conditions.

[Dynamics of the population structure of the Escherichia coli recombinant strain during continuous culture].

PubMed

Popova, L Iu; Lutskaia, N I; Bogucharov, A A; Bril'kov, A V; Pechurkin, N S

1992-01-01

The populational structure of the Escherichia coli strain Z905 containing the recombinant plasmid with the phenotype AprLux+ was studied in chemostat. It was shown that the stability of the ratio of plasmid containing cells and cells without plasmids depends in the first place on the presence of the selective factor (ampicillin) in the medium and on the sources of carbon and energy limiting growth.

Screening For Inhibitors Of Essential Leishmania Glucose Transporters

DTIC Science & Technology

2011-07-01

of biological activities and structural diversity. The library was screened in duplicate employing 13 384-well plates. High, Med, and Low control... Antimalarial drug therapy: the role of parasite biology and drug resis- tance. J Clin Pharmacol 2006;46(12):1487–97. [3] Matovu E, Seebeck T, Enyaru JC...biological activities . Chem Pharm Bull (Tokyo) 1987;35(7):2894–9. 20] Ter Kuile BH, Opperdoes FR. A chemostat study on proline uptake and metabolism of

Laboratory observations of biocide efficiency against Legionella in model cooling tower systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, W.M.; Eccles, J.; Fricker, C.

1999-07-01

The efficacy of specific oxidizing and non-oxidizing biocides was examined using a model cooling system inoculated with a microcosm containing an environmental isolate of Legionella pneumophila. The microcosm was prepared in a two-stage chemostat, which provided a consistent source of microbiological inoculum for the study. The microcosm consisted of both sessile (within biofilms) and planktonic Legionella in association with other microorganisms, including Pseudomonas species and cyst-forming ameobae. A procedure was established to successfully transfer the chemostat grown inoculum to the model cooling system and establish both sessile and planktonic forms of Legionella in the model cooling system. The greatest biocidalmore » effect for all of the biocides was observed immediately after dosing. This effect was relatively short-lived even for the slow acting biocides such isothiazolin (as 8 ppm active) where an effect was only observed over the first 12 hours. The faster acting biocides, DBNPA (as 8 ppm active) and gluteraldehyde (as 27 ppm active), did initially reduce Legionella populations but did not totally eliminate Legionella or provide lasting control. Chlorine and bromine (as 0.5--1.5 ppm free halogen), and ozone (as 0.1--0.5 ppm free reserve) reduced and controlled Legionella populations so long as a free reserve of oxidant was maintained. Legionella recovered quickly after biocide dosing, reestablishing similar levels to those observed before dosing.« less

Characteristics of the Freshwater Cyanobacterium Microcystis aeruginosa Grown in Iron-Limited Continuous Culture

PubMed Central

Dang, T. C.; Fujii, M.; Rose, A. L.; Bligh, M.

2012-01-01

A continuous culturing system (chemostat) made of metal-free materials was successfully developed and used to maintain Fe-limited cultures of Microcystis aeruginosa PCC7806 at nanomolar iron (Fe) concentrations (20 to 50 nM total Fe). EDTA was used to maintain Fe in solution, with bioavailable Fe controlled by absorption of light by the ferric EDTA complex and resultant reduction of Fe(III) to Fe(II). A kinetic model describing Fe transformations and biological uptake was applied to determine the biologically available form of Fe (i.e., unchelated ferrous iron) that is produced by photoreductive dissociation of the ferric EDTA complex. Prediction by chemostat theory modified to account for the light-mediated formation of bioavailable Fe rather than total Fe was in good agreement with growth characteristics of M. aeruginosa under Fe limitation. The cellular Fe quota increased with increasing dilution rates in a manner consistent with the Droop theory. Short-term Fe uptake assays using cells maintained at steady state indicated that M. aeruginosa cells vary their maximum Fe uptake rate (ρmax) depending on the degree of Fe stress. The rate of Fe uptake was lower for cells grown under conditions of lower Fe availability (i.e., lower dilution rate), suggesting that cells in the continuous cultures adjusted to Fe limitation by decreasing ρmax while maintaining a constant affinity for Fe. PMID:22210212

Tragedy of the commons in the chemostat.

PubMed

Schuster, Martin; Foxall, Eric; Finch, David; Smith, Hal; De Leenheer, Patrick

2017-01-01

We present a proof of principle for the phenomenon of the tragedy of the commons that is at the center of many theories on the evolution of cooperation. Whereas the tragedy is commonly set in a game theoretical context, and attributed to an underlying Prisoner's Dilemma, we take an alternative approach based on basic mechanistic principles of species growth that does not rely on the specification of payoffs which may be difficult to determine in practice. We establish the tragedy in the context of a general chemostat model with two species, the cooperator and the cheater. Both species have the same growth rate function and yield constant, but the cooperator allocates a portion of the nutrient uptake towards the production of a public good -the "Commons" in the Tragedy- which is needed to digest the externally supplied nutrient. The cheater on the other hand does not produce this enzyme, and allocates all nutrient uptake towards its own growth. We prove that when the cheater is present initially, both the cooperator and the cheater will eventually go extinct, hereby confirming the occurrence of the tragedy. We also show that without the cheater, the cooperator can survive indefinitely, provided that at least a low level of public good or processed nutrient is available initially. Our results provide a predictive framework for the analysis of cooperator-cheater dynamics in a powerful model system of experimental evolution.

Process control, energy recovery and cost savings in acetic acid wastewater treatment.

PubMed

Vaiopoulou, E; Melidis, P; Aivasidis, A

2011-02-28

An anaerobic fixed bed loop (AFBL) reactor was applied for treatment of acetic acid (HAc) wastewater. Two pH process control concepts were investigated; auxostatic and chemostatic control. In the auxostatic pH control, feed pump is interrupted when pH falls below a certain pH value in the bioreactor, which results in reactor operation at maximum load. Chemostatic control assures alkaline conditions by setting a certain pH value in the influent, preventing initial reactor acidification. The AFBL reactor treated HAc wastewater at low hydraulic residence time (HRT) (10-12 h), performed at high space time loads (40-45 kg COD/m(3) d) and high space time yield (30-35 kg COD/m(3) d) to achieve high COD (Chemical Oxygen Demand) removal (80%). Material and cost savings were accomplished by utilizing the microbial potential for wastewater neutralization during anaerobic treatment along with application of favourable pH-auxostatic control. NaOH requirement for neutralization was reduced by 75% and HRT was increased up to 20 h. Energy was recovered by applying costless CO(2) contained in the biogas for neutralization of alkaline wastewater. Biogas was enriched in methane by 4 times. This actually brings in more energy profits, since biogas extra heating for CO(2) content during biogas combustion is minimized and usage of other acidifying agents is omitted. Copyright © 2010 Elsevier B.V. All rights reserved.

Physiological and Proteomic Adaptation of “Aromatoleum aromaticum” EbN1 to Low Growth Rates in Benzoate-Limited, Anoxic Chemostats

PubMed Central

Trautwein, Kathleen; Lahme, Sven; Wöhlbrand, Lars; Feenders, Christoph; Mangelsdorf, Kai; Harder, Jens; Steinbüchel, Alexander; Blasius, Bernd; Reinhardt, Richard

2012-01-01

“Aromatoleum aromaticum” EbN1 was cultivated at different growth rates in benzoate-limited chemostats under nitrate-reducing conditions. Physiological characteristics, proteome dynamics, phospholipid-linked fatty acid (PLFA) composition, and poly(3-hydroxybutyrate) (PHB) content were analyzed in steady-state cells at low (μlow) (0.036 h−1), medium (μmed) (0.108 h−1), and high (μhigh) (0.180 h−1) growth rates. A positive correlation to growth rate was observed for cellular parameters (cell size, and DNA and protein contents). The free energy consumed for biomass formation steadily increased with growth rate. In contrast, the energy demand for maintenance increased only from μlow to μmed and then remained constant until μhigh. The most comprehensive proteomic changes were observed at μlow compared to μhigh. Uniformly decreased abundances of protein components of the anaerobic benzoyl coenzyme A (benzoyl-CoA) pathway, central carbon metabolism, and information processing agree with a general deceleration of benzoate metabolism and cellular processes in response to slow growth. In contrast, increased abundances were observed at μlow for diverse catabolic proteins and components of uptake systems in the absence of the respective substrate (aromatic or aliphatic compounds) and for proteins involved in stress responses. This potential catabolic versatility and stress defense during slow growth may be interpreted as preparation for future needs. PMID:22366417

Effect of Nitrogen Source on Growth and Trichloroethylene Degradation by Methane-Oxidizing Bacteria

PubMed Central

Chu, Kung-Hui; Alvarez-Cohen, Lisa

1998-01-01

The effect of nitrogen source on methane-oxidizing bacteria with respect to cellular growth and trichloroethylene (TCE) degradation ability were examined. One mixed chemostat culture and two pure type II methane-oxidizing strains, Methylosinus trichosporium OB3b and strain CAC-2, which was isolated from the chemostat culture, were used in this study. All cultures were able to grow with each of three different nitrogen sources: ammonia, nitrate, and molecular nitrogen. Both M. trichosporium OB3b and strain CAC-2 showed slightly lower net cellular growth rates and cell yields but exhibited higher methane uptake rates, levels of poly-β-hydroxybutyrate (PHB) production, and naphthalene oxidation rates when grown under nitrogen-fixing conditions. The TCE-degrading ability of each culture was measured in terms of initial TCE oxidation rates and TCE transformation capacities (mass of TCE degraded/biomass inactivated), measured both with and without external energy sources. Higher initial TCE oxidation rates and TCE transformation capacities were observed in nitrogen-fixing mixed, M. trichosporium OB3b, and CAC-2 cultures than in nitrate- or ammonia-supplied cells. TCE transformation capacities were found to correlate with cellular PHB content in all three cultures. The results of this study suggest that the nitrogen-fixing capabilities of methane-oxidizing bacteria can be used to select for high-activity TCE degraders for the enhancement of bioremediation in fixed-nitrogen-limited environments. PMID:9726896

Kinetics of butyrate, acetate, and hydrogen metabolism in a thermophilic, anaerobic, butyrate-degrading triculture.

PubMed

Ahring, B K; Westermann, P

1987-02-01

Kinetics of butyrate, acetate, and hydrogen metabolism were determined with butyrate-limited, chemostat-grown tricultures of a thermophilic butyrate-utilizing bacterium together with Methanobacterium thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic rod. Kinetic parameters were determined from progress curves fitted to the integrated form of the Michaelis-Menten equation. The apparent half-saturation constants, K(m), for butyrate, acetate, and dissolved hydrogen were 76 muM, 0.4 mM, and 8.5 muM, respectively. Butyrate and hydrogen were metabolized to a concentration of less than 1 muM, whereas acetate uptake usually ceased at a concentration of 25 to 75 muM, indicating a threshold level for acetate uptake. No significant differences in K(m) values for butyrate degradation were found between chemostat- and batch-grown tricultures, although the maximum growth rate was somewhat higher in the batch cultures in which the medium was supplemented with yeast extract. Acetate utilization was found to be the rate-limiting reaction for complete degradation of butyrate to methane and carbon dioxide in continuous culture. Increasing the dilution rate resulted in a gradual accumulation of acetate. The results explain the low concentrations of butyrate and hydrogen normally found during anaerobic digestion and the observation that acetate is the first volatile fatty acid to accumulate upon a decrease in retention time or increase in organic loading of a digestor.

Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture.

PubMed

Nahku, Ranno; Peebo, Karl; Valgepea, Kaspar; Barrick, Jeffrey E; Adamberg, Kaarel; Vilu, Raivo

2011-09-01

Nutrient-limited continuous cultures in chemostats have been used to study microbial cell physiology for over 60 years. Genome instability and genetic heterogeneity are possible uncontrolled factors in continuous cultivation experiments. We investigated these issues by using high-throughput (HT) DNA sequencing to characterize samples from different phases of a glucose-limited accelerostat (A-stat) experiment with Escherichia coli K-12 MG1655 and a duration regularly used in cell physiology studies (20 generations of continuous cultivation). Seven consensus mutations from the reference sequence and five subpopulations characterized by different mutations were detected in the HT-sequenced samples. This genetic heterogeneity was confirmed to result from the stock culture by Sanger sequencing. All the subpopulations in which allele frequencies increased (betA, cspG/cspH, glyA) during the experiment were also present at the end of replicate A-stats, indicating that no new subpopulations emerged during our experiments. The fact that ~31 % of the cells in our initial cultures obtained directly from a culture stock centre were mutants raises concerns that even if cultivations are started from single colonies, there is a significant chance of picking a mutant clone with an altered phenotype. Our results show that current HT DNA sequencing technology allows accurate subpopulation analysis and demonstrates that a glucose-limited E. coli K-12 MG1655 A-stat experiment with a duration of tens of generations is suitable for studying cell physiology and collecting quantitative data for metabolic modelling without interference from new mutations.

Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture

PubMed Central

Nahku, Ranno; Peebo, Karl; Valgepea, Kaspar; Barrick, Jeffrey E.; Adamberg, Kaarel

2011-01-01

Nutrient-limited continuous cultures in chemostats have been used to study microbial cell physiology for over 60 years. Genome instability and genetic heterogeneity are possible uncontrolled factors in continuous cultivation experiments. We investigated these issues by using high-throughput (HT) DNA sequencing to characterize samples from different phases of a glucose-limited accelerostat (A-stat) experiment with Escherichia coli K-12 MG1655 and a duration regularly used in cell physiology studies (20 generations of continuous cultivation). Seven consensus mutations from the reference sequence and five subpopulations characterized by different mutations were detected in the HT-sequenced samples. This genetic heterogeneity was confirmed to result from the stock culture by Sanger sequencing. All the subpopulations in which allele frequencies increased (betA, cspG/cspH, glyA) during the experiment were also present at the end of replicate A-stats, indicating that no new subpopulations emerged during our experiments. The fact that ~31 % of the cells in our initial cultures obtained directly from a culture stock centre were mutants raises concerns that even if cultivations are started from single colonies, there is a significant chance of picking a mutant clone with an altered phenotype. Our results show that current HT DNA sequencing technology allows accurate subpopulation analysis and demonstrates that a glucose-limited E. coli K-12 MG1655 A-stat experiment with a duration of tens of generations is suitable for studying cell physiology and collecting quantitative data for metabolic modelling without interference from new mutations. PMID:21700661

Growth of Coccolithophores Controlled by Internal Nutrient Stores in Light- and Nutrient-Limited Batch Reactors: Relevance for the BIOSOPE Deep Ecological Niche of Coccolithophores.

NASA Astrophysics Data System (ADS)

Laura, P.; Probert, I.; Langer, G.; Aloisi, G.

2016-02-01

Coccolithophores are unicellular, calcifying marine algae that play a fundamental role in the oceanic carbon cycle. Recent research has focused on investigating the effect of ocean acidification on cellular calcification. However, the success of this important phytoplankton group in the future ocean will depend on how cellular growth reacts to changes in a combination of environmental variables. We carried out batch culture experiments in conditions of light- and nutrient- (nitrate and phosphate) limitation that reproduce the in situ conditions of a deep ecological niche of coccolithophores in the South Pacific Gyre (BIOSOPE cruise, 2004). We modelled nutrient acquisition and cellular growth in our batch experiments using a Droop internal-stores model. We show that nutrient acquisition and growth are decoupled in coccolithophores; this ability may be key in making life possible in oligotrophic conditions such as the deep BIOSOPE biological niche. Combining the results of our culture experiments with those of Langer et al. (2013), we used the model to obtain estimates of fundamental physiological parameters such as the Monod constant for nutrient uptake, the maximum growth rate and the minimum cellular nutrient quota. These parameters are characteristic of different phytoplankton groups and are needed to simulate phytoplankton growth in biogeochemical models. Our results suggest that growth of coccolithophores in the BIOSOPE deep ecological niche is light-limited rather than nutrient-limited. Our work also shows that simple batch experiments and straightforward numerical modelling are capable of providing estimates of physiological parameters usually obtained in more costly and complicated chemostat experiments.

[MODIS Investigation

NASA Technical Reports Server (NTRS)

Abbott, Mark R.

1998-01-01

The objectives of the last six months were: (1) Revise the algorithms for the Fluorescence Line Height (FLH) and Chlorophyll Fluorescence Efficiency (CFE) products, especially the data quality flags; (2) Revise the MOCEAN validation plan; (3) Deploy and recover bio-optical instrumentation at the Hawaii Ocean Time-series (HOT) site as part of the Joint Global Ocean Flux Study (JGOFS); (4) Prepare for field work in the Antarctic Polar Frontal Zone as part of JGOFS; (5) Submit manuscript on bio-optical time scales as estimated from Lagrangian drifters; (6) Conduct chemostat experiments on fluorescence; (7) Interface with the Global Imager (GLI) science team; and (8) Continue development of advanced data system browser. We are responsible for the delivery of two at-launch products for AM-1: Fluorescence line height (FLH) and chlorophyll fluorescence efficiency (CFE). We also considered revising the input chlorophyll, which is used to determine the degree of binning. We have refined the quality flags for the Version 2 algorithms. We have acquired and installed a Silicon Graphics Origin 200. We are working with the University of Miami team to develop documentation that will describe how the MODIS ocean components are linked together.

Genetic segregation in a high-yielding streptomycin-producing strain of Streptomyces griseus.

PubMed

Roth, M; Schwalenberg, B; Reiche, R; Noack, D; Geuther, R; Eritt, I

1982-01-01

The streptomycin-producing Streptomyces griseus HP spontaneously segregated non-reverting derivatives with altered phenotypes. Clones characterized by increased spore formation and decreased streptomycin production were found. Two other types of derivatives were defective in aerial mycelium and streptomycin formation as well, but differed in the capacity to synthesize a yellow pigment. These derivatives were examined with respect to further properties. The stability of S. griseus HP was investigated in relation to conditions of continuous culture. Both at 26 and 30 degrees C, under glycerol and NH4Cl limitation a rapid segregation and enrichment of streptomycin-non-producing derivatives occurred. At 34 degrees C and glycerol limitation segregation began only after about 35 generations of continuous culture. In NH4Cl-limited chemostats the original strain was stable during 80 generations. In the course of the continuous culture experiments it was shown that the onset of genetic segregation within mycelia can be detected before it becomes obvious in colonies grown from the mycelia. This was achieved by fractionation of the mycelia by protoplast formation and subsequent plating on regeneration medium allowing colony growth and differentiation.

Dynamic model of temperature impact on cell viability and major product formation during fed-batch and continuous ethanolic fermentation in Saccharomyces cerevisiae.

PubMed

Amillastre, Emilie; Aceves-Lara, César-Arturo; Uribelarrea, Jean-Louis; Alfenore, Sandrine; Guillouet, Stéphane E

2012-08-01

The impact of the temperature on an industrial yeast strain was investigated in very high ethanol performance fermentation fed-batch process within the range of 30-47 °C. As previously observed with a lab strain, decoupling between growth and glycerol formation occurred at temperature of 36 °C and higher. A dynamic model was proposed to describe the impact of the temperature on the total and viable biomass, ethanol and glycerol production. The model validation was implemented with experimental data sets from independent cultures under different temperatures, temperature variation profiles and cultivation modes. The proposed model fitted accurately the dynamic evolutions for products and biomass concentrations over a wide range of temperature profiles. R2 values were above 0.96 for ethanol and glycerol in most experiments. The best results were obtained at 37 °C in fed-batch and chemostat cultures. This dynamic model could be further used for optimizing and monitoring the ethanol fermentation at larger scale. Copyright © 2012 Elsevier Ltd. All rights reserved.

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polettini, Matteo, E-mail: matteo.polettini@uni.lu; Esposito, Massimiliano

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulatedmore » by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s{sup Y} between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s{sup Y}. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.« less

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws.

PubMed

Polettini, Matteo; Esposito, Massimiliano

2014-07-14

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s(Y) between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s(Y). We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

Single-Cell Microfluidics to Study the Effects of Genome Deletion on Bacterial Growth Behavior.

PubMed

Yuan, Xiaofei; Couto, Jillian M; Glidle, Andrew; Song, Yanqing; Sloan, William; Yin, Huabing

2017-12-15

By directly monitoring single cell growth in a microfluidic platform, we interrogated genome-deletion effects in Escherichia coli strains. We compared the growth dynamics of a wild type strain with a clean genome strain, and their derived mutants at the single-cell level. A decreased average growth rate and extended average lag time were found for the clean genome strain, compared to those of the wild type strain. Direct correlation between the growth rate and lag time of individual cells showed that the clean genome population was more heterogeneous. Cell culturability (the ratio of growing cells to the sum of growing and nongrowing cells) of the clean genome population was also lower. Interestingly, after the random mutations induced by a glucose starvation treatment, for the clean genome population mutants that had survived the competition of chemostat culture, each parameter markedly improved (i.e., the average growth rate and cell culturability increased, and the lag time and heterogeneity decreased). However, this effect was not seen in the wild type strain; the wild type mutants cultured in a chemostat retained a high diversity of growth phenotypes. These results suggest that quasi-essential genes that were deleted in the clean genome might be required to retain a diversity of growth characteristics at the individual cell level under environmental stress. These observations highlight that single-cell microfluidics can reveal subtle individual cellular responses, enabling in-depth understanding of the population.

Catchment heterogeneity controls emergent archetype concentration-discharge relationships

NASA Astrophysics Data System (ADS)

Musolff, A.; Fleckenstein, J. H.; Rao, P. S.; Jawitz, J. W.

2017-12-01

Relationships between in-stream dissolved solute concentrations (C) and discharge (Q) are often-used indicators of catchment-scale processes and their interference with human activities. Here we analyze observational C-Q relationships from 61 catchments and 8 different solutes across a wide range of land-uses and discharge regimes. This analysis is combined with a parsimonious stochastic modeling approach to test how C-Q relationships arise from spatial heterogeneity in catchment solute sources coupled with different timescales of biogeochemical reactions. The observational data exhibit archetypical dilution, enrichment, and constant C-Q patterns. Moreover, with land-use intensification we find decreasing C variability relative to Q variability (chemostatic export regime). Our model indicates that the dominant driver of emergent C-Q patterns was structured heterogeneity of solute sources implemented as correlation of source concentration to travel time. Regardless of the C-Q pattern, with decreasing source heterogeneity we consistently find lower variability in C than in Q and a dominance of chemostatic export regimes. Here, the variance in exported loads is determined primarily by variance of Q. We conclude that efforts to improve stream water quality and ecological integrity in intensely managed catchments should lead away from landscape homogenization by introducing structured source heterogeneity. References: Musolff, A., J. H. Fleckenstein, P. S. C. Rao, and J. W. Jawitz (2017), Emergent archetype patterns of coupled hydrologic and biogeochemical responses in catchments, Geophys. Res. Lett., 44(9), 4143-4151, doi: 10.1002/2017GL072630.

Light-field-characterization in a continuous hydrogen-producing photobioreactor by optical simulation and computational fluid dynamics.

PubMed

Krujatz, Felix; Illing, Rico; Krautwer, Tobias; Liao, Jing; Helbig, Karsten; Goy, Katharina; Opitz, Jörg; Cuniberti, Gianaurelio; Bley, Thomas; Weber, Jost

2015-12-01

Externally illuminated photobioreactors (PBRs) are widely used in studies on the use of phototrophic microorganisms as sources of bioenergy and other photobiotechnology research. In this work, straightforward simulation techniques were used to describe effects of varying fluid flow conditions in a continuous hydrogen-producing PBR on the rate of photofermentative hydrogen production (rH2 ) by Rhodobacter sphaeroides DSM 158. A ZEMAX optical ray tracing simulation was performed to quantify the illumination intensity reaching the interior of the cylindrical PBR vessel. 24.2% of the emitted energy was lost through optical effects, or did not reach the PBR surface. In a dense culture of continuously producing bacteria during chemostatic cultivation, the illumination intensity became completely attenuated within the first centimeter of the PBR radius as described by an empirical three-parametric model implemented in Mathcad. The bacterial movement in chemostatic steady-state conditions was influenced by varying the fluid Reynolds number. The "Computational Fluid Dynamics" and "Particle Tracing" tools of COMSOL Multiphysics were used to visualize the fluid flow pattern and cellular trajectories through well-illuminated zones near the PBR periphery and dark zones in the center of the PBR. A moderate turbulence (Reynolds number = 12,600) and fluctuating illumination of 1.5 Hz were found to yield the highest continuous rH2 by R. sphaeroides DSM 158 (170.5 mL L(-1) h(-1) ) in this study. © 2015 Wiley Periodicals, Inc.

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

NASA Astrophysics Data System (ADS)

Polettini, Matteo; Esposito, Massimiliano

2014-07-01

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = sY between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats sY. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

Short-term dynamic behavior of Escherichia coli in response to successive glucose pulses on glucose-limited chemostat cultures.

PubMed

Sunya, Sirichai; Bideaux, Carine; Molina-Jouve, Carole; Gorret, Nathalie

2013-04-15

The effect of repeated glucose perturbations on dynamic behavior of Escherichia coli DPD2085, yciG::LuxCDABE reporter strain, was studied and characterized on a short-time scale using glucose-limited chemostat cultures at dilution rates close to 0.18h(-1). The substrate disturbances were applied on independent steady-state cultures, firstly using a single glucose pulse under different aeration conditions and secondly using repeated glucose pulses under fully aerobic condition. The dynamic responses of E. coli to a single glucose pulse of different intensities (0.25 and 0.6gL(-1)) were significantly similar at macroscopic level, revealing the independency of the macroscopic microbial behavior to the perturbation intensity in the range of tested glucose concentrations. The dynamic responses of E. coli to repeated glucose pulses to simulate fluctuating environments between glucose-limited and glucose-excess conditions were quantified; similar behavior regarding respiration and by-product formations was observed, except for the first perturbation denoted by an overshoot of the specific oxygen uptake rate in the first minutes after the pulse. In addition, transcriptional induction of yciG promoter gene involved in general stress response, σ(S), was monitored through the bioluminescent E. coli strain. This study aims to provide and compare short-term quantitative kinetics data describing the dynamic behavior of E. coli facing repeated transient substrate conditions. Copyright © 2013 Elsevier B.V. All rights reserved.

Prolonged Maltose-Limited Cultivation of Saccharomyces cerevisiae Selects for Cells with Improved Maltose Affinity and Hypersensitivity

PubMed Central

Jansen, Mickel L. A.; Daran-Lapujade, Pascale; de Winde, Johannes H.; Piper, Matthew D. W.; Pronk, Jack T.

2004-01-01

Prolonged cultivation (>25 generations) of Saccharomyces cerevisiae in aerobic, maltose-limited chemostat cultures led to profound physiological changes. Maltose hypersensitivity was observed when cells from prolonged cultivations were suddenly exposed to excess maltose. This substrate hypersensitivity was evident from massive cell lysis and loss of viability. During prolonged cultivation at a fixed specific growth rate, the affinity for the growth-limiting nutrient (i.e., maltose) increased, as evident from a decreasing residual maltose concentration. Furthermore, the capacity of maltose-dependent proton uptake increased up to 2.5-fold during prolonged cultivation. Genome-wide transcriptome analysis showed that the increased maltose transport capacity was not primarily due to increased transcript levels of maltose-permease genes upon prolonged cultivation. We propose that selection for improved substrate affinity (ratio of maximum substrate consumption rate and substrate saturation constant) in maltose-limited cultures leads to selection for cells with an increased capacity for maltose uptake. At the same time, the accumulative nature of maltose-proton symport in S. cerevisiae leads to unrestricted uptake when maltose-adapted cells are exposed to a substrate excess. These changes were retained after isolation of individual cell lines from the chemostat cultures and nonselective cultivation, indicating that mutations were involved. The observed trade-off between substrate affinity and substrate tolerance may be relevant for metabolic engineering and strain selection for utilization of substrates that are taken up by proton symport. PMID:15066785

Growth of the coccolithophore Emiliania huxleyi in light- and nutrient-limited batch reactors: relevance for the BIOSOPE deep ecological niche of coccolithophores

NASA Astrophysics Data System (ADS)

Perrin, Laura; Probert, Ian; Langer, Gerald; Aloisi, Giovanni

2016-11-01

Coccolithophores are unicellular calcifying marine algae that play an important role in the oceanic carbon cycle via their cellular processes of photosynthesis (a CO2 sink) and calcification (a CO2 source). In contrast to the well-studied, surface-water coccolithophore blooms visible from satellites, the lower photic zone is a poorly known but potentially important ecological niche for coccolithophores in terms of primary production and carbon export to the deep ocean. In this study, the physiological responses of an Emiliania huxleyi strain to conditions simulating the deep niche in the oligotrophic gyres along the BIOSOPE transect in the South Pacific Gyre were investigated. We carried out batch culture experiments with an E. huxleyi strain isolated from the BIOSOPE transect, reproducing the in situ conditions of light and nutrient (nitrate and phosphate) limitation. By simulating coccolithophore growth using an internal stores (Droop) model, we were able to constrain fundamental physiological parameters for this E. huxleyi strain. We show that simple batch experiments, in conjunction with physiological modelling, can provide reliable estimates of fundamental physiological parameters for E. huxleyi that are usually obtained experimentally in more time-consuming and costly chemostat experiments. The combination of culture experiments, physiological modelling and in situ data from the BIOSOPE cruise show that E. huxleyi growth in the deep BIOSOPE niche is limited by availability of light and nitrate. This study contributes more widely to the understanding of E. huxleyi physiology and behaviour in a low-light and oligotrophic environment of the ocean.

In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments.

PubMed

Deshmukh, Amit T; Verheijen, Peter J T; Maleki Seifar, Reza; Heijnen, Joseph J; van Gulik, Walter M

2015-11-01

In this study we combined experimentation with mathematical modeling to unravel the in vivo kinetic properties of the enzymes and transporters of the penicillin biosynthesis pathway in a high yielding Penicillium chrysogenum strain. The experiment consisted of a step response experiment with the side chain precursor phenyl acetic acid (PAA) in a glucose-limited chemostat. The metabolite data showed that in the absence of PAA all penicillin pathway enzymes were expressed, leading to the production of a significant amount of 6-aminopenicillanic acid (6APA) as end product. After the stepwise perturbation with PAA, the pathway produced PenG within seconds. From the extra- and intracellular metabolite measurements, hypotheses for the secretion mechanisms of penicillin pathway metabolites were derived. A dynamic model of the penicillin biosynthesis pathway was then constructed that included the formation and transport over the cytoplasmic membrane of pathway intermediates, PAA and the product penicillin-G (PenG). The model parameters and changes in the enzyme levels of the penicillin biosynthesis pathway under in vivo conditions were simultaneously estimated using experimental data obtained at three different timescales (seconds, minutes, hours). The model was applied to determine changes in the penicillin pathway enzymes in time, calculate fluxes and analyze the flux control of the pathway. This led to a reassessment of the in vivo behavior of the pathway enzymes and in particular Acyl-CoA:Isopenicillin N Acyltransferase (AT). Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

PubMed Central

Yoon, Sung Ho; Turkarslan, Serdar; Reiss, David J.; Pan, Min; Burn, June A.; Costa, Kyle C.; Lie, Thomas J.; Slagel, Joseph; Moritz, Robert L.; Hackett, Murray; Leigh, John A.; Baliga, Nitin S.

2013-01-01

Methanogens catalyze the critical methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and noncoding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 58 different steady-state and time-course experiments that were performed in chemostats or batch cultures under a spectrum of environmental perturbations that modulated methanogenesis. Analyses of the EGRIN model have revealed novel components of methanogenesis that included at least three additional protein-coding genes of previously unknown function as well as one noncoding RNA. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to intercoordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel transcription factors in the regulation of phosphate-dependent repression of formate dehydrogenase—a key enzyme in the methanogenesis pathway. The EGRIN model demonstrates regulatory affiliations within methanogenesis as well as between methanogenesis and other cellular functions. PMID:24089473

Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse.

PubMed

Wu, Liang; van Dam, Jan; Schipper, Dick; Kresnowati, M T A Penia; Proell, Angela M; Ras, Cor; van Winden, Wouter A; van Gulik, Walter M; Heijnen, Joseph J

2006-05-01

The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O(2) uptake and CO(2) evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO(2) evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.

Transcriptome-Based Characterization of Interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in Lactose-Grown Chemostat Cocultures

PubMed Central

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J. H.; Luttik, Marijke A. H.; Pronk, Jack T.; Smid, Eddy J.; Bron, Peter A.

2013-01-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations. PMID:23872557

Physiological and Proteomic Analysis of Escherichia coli Iron-Limited Chemostat Growth

PubMed Central

Folsom, James Patrick; Parker, Albert E.

2014-01-01

Iron bioavailability is a major limiter of bacterial growth in mammalian host tissue and thus represents an important area of study. Escherichia coli K-12 metabolism was studied at four levels of iron limitation in chemostats using physiological and proteomic analyses. The data documented an E. coli acclimation gradient where progressively more severe iron scarcity resulted in a larger percentage of substrate carbon being directed into an overflow metabolism accompanied by a decrease in biomass yield on glucose. Acetate was the primary secreted organic by-product for moderate levels of iron limitation, but as stress increased, the metabolism shifted to secrete primarily lactate (∼70% of catabolized glucose carbon). Proteomic analysis reinforced the physiological data and quantified relative increases in glycolysis enzyme abundance and decreases in tricarboxylic acid (TCA) cycle enzyme abundance with increasing iron limitation stress. The combined data indicated that E. coli responds to limiting iron by investing the scarce resource in essential enzymes, at the cost of catabolic efficiency (i.e., downregulating high-ATP-yielding pathways containing enzymes with large iron requirements, like the TCA cycle). Acclimation to iron-limited growth was contrasted experimentally with acclimation to glucose-limited growth to identify both general and nutrient-specific acclimation strategies. While the iron-limited cultures maximized biomass yields on iron and increased expression of iron acquisition strategies, the glucose-limited cultures maximized biomass yields on glucose and increased expression of carbon acquisition strategies. This study quantified ecologically competitive acclimations to nutrient limitations, yielding knowledge essential for understanding medically relevant bacterial responses to host and to developing intervention strategies. PMID:24837288

Concentration-discharge relationships reflect chemostatic characteristics of US catchments

USGS Publications Warehouse

Godsey, S.E.; Kirchner, J.W.; Clow, D.W.

2009-01-01

Concentration-discharge relationships have been widely used as clues to the hydrochemical processes that control runoff chemistry. Here we examine concentration-discharge relationships for solutes produced primarily by mineral weathering in 59 geochemically diverse US catchments. We show that these catchments exhibit nearly chemostatic behaviour; their stream concentrations of weathering products such as Ca, Mg, Na, and Si typically vary by factors of only 3 to 20 while discharge varies by several orders of magnitude. Similar patterns are observed at the inter-annual time scale. This behaviour implies that solute concentrations in stream water are not determined by simple dilution of a fixed solute flux by a variable flux of water, and that rates of solute production and/or mobilization must be nearly proportional to water fluxes, both on storm and inter-annual timescales. We compared these catchments' concentration-discharge relationships to the predictions of several simple hydrological and geochemical models. Most of these models can be forced to approximately fit the observed concentration-discharge relationships, but often only by assuming unrealistic or internally inconsistent parameter values. We propose a new model that also fits the data and may be more robust. We suggest possible tests of the new model for future studies. The relative stability of concentration under widely varying discharge may help make aquatic environments habitable. It also implies that fluxes of weathering solutes in streams, and thus fluxes of alkalinity to the oceans, are determined primarily by water fluxes. Thus, hydrology may be a major driver of the ocean-alkalinity feedback regulating climate change. Copyright ?? 2009 John Wiley & Sons, Ltd.

Metabolic engineering of β-oxidation in Penicillium chrysogenum for improved semi-synthetic cephalosporin biosynthesis.

PubMed

Veiga, Tânia; Gombert, Andreas K; Landes, Nils; Verhoeven, Maarten D; Kiel, Jan A K W; Krikken, Arjen M; Nijland, Jeroen G; Touw, Hesselien; Luttik, Marijke A H; van der Toorn, John C; Driessen, Arnold J M; Bovenberg, Roel A L; van den Berg, Marco A; van der Klei, Ida J; Pronk, Jack T; Daran, Jean-Marc

2012-07-01

Industrial production of semi-synthetic cephalosporins by Penicillium chrysogenum requires supplementation of the growth media with the side-chain precursor adipic acid. In glucose-limited chemostat cultures of P. chrysogenum, up to 88% of the consumed adipic acid was not recovered in cephalosporin-related products, but used as an additional carbon and energy source for growth. This low efficiency of side-chain precursor incorporation provides an economic incentive for studying and engineering the metabolism of adipic acid in P. chrysogenum. Chemostat-based transcriptome analysis in the presence and absence of adipic acid confirmed that adipic acid metabolism in this fungus occurs via β-oxidation. A set of 52 adipate-responsive genes included six putative genes for acyl-CoA oxidases and dehydrogenases, enzymes responsible for the first step of β-oxidation. Subcellular localization of the differentially expressed acyl-CoA oxidases and dehydrogenases revealed that the oxidases were exclusively targeted to peroxisomes, while the dehydrogenases were found either in peroxisomes or in mitochondria. Deletion of the genes encoding the peroxisomal acyl-CoA oxidase Pc20g01800 and the mitochondrial acyl-CoA dehydrogenase Pc20g07920 resulted in a 1.6- and 3.7-fold increase in the production of the semi-synthetic cephalosporin intermediate adipoyl-6-APA, respectively. The deletion strains also showed reduced adipate consumption compared to the reference strain, indicating that engineering of the first step of β-oxidation successfully redirected a larger fraction of adipic acid towards cephalosporin biosynthesis. Copyright © 2012 Elsevier Inc. All rights reserved.

Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures.

PubMed

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J H; Luttik, Marijke A H; Pronk, Jack T; Smid, Eddy J; Bron, Peter A; Daran-Lapujade, Pascale

2013-10-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations.

Biodegradation of individual and multiple chlorinated aliphatic hydrocarbons by methane-oxidizing cultures.

PubMed Central

Chang, H L; Alvarez-Cohen, L

1996-01-01

The microbial degradation of chlorinated and nonchlorinated methanes, ethanes, and ethanes by a mixed methane-oxidizing culture grown under chemostat and batch conditions is evaluated and compared with that by two pure methanotrophic strains: CAC1 (isolated from the mixed culture) and Methylosinus trichosporium OB3b. With the exception of 1,1-dichloroethylene, the transformation capacity (Tc) for each chlorinated aliphatic hydrocarbon was generally found to be in inverse proportion to its chlorine content within each aliphatic group (i.e., methanes, ethanes, and ethenes), whereas similar trends were not observed for degradation rate constants. Tc trends were similar for all methane-oxidizing cultures tested. None of the cultures were able to degrade the fully chlorinated aliphatics such as perchloroethylene and carbon tetrachloride. Of the four cultures tested, the chemostat-grown mixed culture exhibited the highest Tc for trichloroethylene, cis-1,2-dichloroethylene, tetrachloroethane, 1,1,1-trichloroethane, and 1,2-dichloroethane, whereas the pure batch-grown OB3b culture exhibited the highest Tc for all other compounds tested. The product toxicity of chlorinated aliphatic hydrocarbons in a mixture containing multiple compounds was cumulative and predictable when using parameters measured from the degradation of individual compounds. The Tc for each chlorinated aliphatic hydrocarbon in a mixture (Tcmix) and the total Tc for the mixture (sigma Tcmix) are functions of the individual Tc, the initial substrate concentration (S0), and the first-order rate constant (k/Ks) of each compound in the mixture, indicating the importance of identifying the properties and compositions of all potentially degradable compounds in a contaminant mixture. PMID:8795228

Primary weathering rates, water transit times and concentration-discharge relations: A theoretical analysis for the critical zone

NASA Astrophysics Data System (ADS)

Ameli, Ali; Erlandsson, Martin; Beven, Keith; Creed, Irena; McDonnell, Jeffrey; Bishop, Kevin

2017-04-01

The permeability architecture of the critical zone exerts a major influence on the hydrogeochemistry of the critical zone. Water flowpath dynamics drive the spatio-temporal pattern of geochemical evolution and resulting streamflow concentration-discharge (C-Q) relation, but these flowpaths are complex and difficult to map quantitatively. Here, we couple a new integrated flow and particle tracking transport model with a general reversible Transition-State-Theory style dissolution rate-law to explore theoretically how C-Q relations and concentration in the critical zone respond to decline in saturated hydraulic conductivity (Ks) with soil depth. We do this for a range of flow rates and mineral reaction kinetics. Our results show that for minerals with a high ratio of equilibrium concentration to intrinsic weathering rate, vertical heterogeneity in Ks enhances the gradient of weathering-derived solute concentration in the critical zone and strengthens the inverse stream C-Q relation. As the ratio of equilibrium concentration to intrinsic weathering rate decreases, the spatial distribution of concentration in the critical zone becomes more uniform for a wide range of flow rates, and stream C-Q relation approaches chemostatic behaviour, regardless of the degree of vertical heterogeneity in Ks. These findings suggest that the transport-controlled mechanisms in the hillslope can lead to chemostatic C-Q relations in the stream while the hillslope surface reaction-controlled mechanisms are associated with an inverse stream C-Q relation. In addition, as the ratio of equilibrium concentration to intrinsic weathering rate decreases, the concentration in the critical zone and stream become less dependent on groundwater age (or transit time)

Primary weathering rates, water transit times, and concentration-discharge relations: A theoretical analysis for the critical zone

NASA Astrophysics Data System (ADS)

Ameli, Ali A.; Beven, Keith; Erlandsson, Martin; Creed, Irena F.; McDonnell, Jeffrey J.; Bishop, Kevin

2017-01-01

The permeability architecture of the critical zone exerts a major influence on the hydrogeochemistry of the critical zone. Water flow path dynamics drive the spatiotemporal pattern of geochemical evolution and resulting streamflow concentration-discharge (C-Q) relation, but these flow paths are complex and difficult to map quantitatively. Here we couple a new integrated flow and particle tracking transport model with a general reversible Transition State Theory style dissolution rate law to explore theoretically how C-Q relations and concentration in the critical zone respond to decline in saturated hydraulic conductivity (Ks) with soil depth. We do this for a range of flow rates and mineral reaction kinetics. Our results show that for minerals with a high ratio of equilibrium concentration (Ceq) to intrinsic weathering rate (Rmax), vertical heterogeneity in Ks enhances the gradient of weathering-derived solute concentration in the critical zone and strengthens the inverse stream C-Q relation. As CeqRmax decreases, the spatial distribution of concentration in the critical zone becomes more uniform for a wide range of flow rates, and stream C-Q relation approaches chemostatic behavior, regardless of the degree of vertical heterogeneity in Ks. These findings suggest that the transport-controlled mechanisms in the hillslope can lead to chemostatic C-Q relations in the stream while the hillslope surface reaction-controlled mechanisms are associated with an inverse stream C-Q relation. In addition, as CeqRmax decreases, the concentration in the critical zone and stream become less dependent on groundwater age (or transit time).

A potential mechanism of energy-metabolism oscillation in an aerobic chemostat culture of the yeast Saccharomyces cerevisiae.

PubMed

Xu, Zhaojun; Tsurugi, Kunio

2006-04-01

The energy-metabolism oscillation in aerobic chemostat cultures of yeast is a periodic change of the respiro-fermentative and respiratory phase. In the respiro-fermentative phase, the NADH level was kept high and respiration was suppressed, and glucose was anabolized into trehalose and glycogen at a rate comparable to that of catabolism. On the transition to the respiratory phase, cAMP levels increased triggering the breakdown of storage carbohydrates and the increased influx of glucose into the glycolytic pathway activated production of glycerol and ethanol consuming NADH. The resulting increase in the NAD(+)/NADH ratio stimulated respiration in combination with a decrease in the level of ATP, which was consumed mainly in the formation of biomass accompanying budding, and the accumulated ethanol and glycerol were gradually degraded by respiration via NAD(+)-dependent oxidation to acetate and the respiratory phase ceased after the recovery of NADH and ATP levels. However, the mRNA levels of both synthetic and degradative enzymes of storage carbohydrates were increased around the early respiro-fermentative phase, when storage carbohydrates are being synthesized, suggesting that the synthetic enzymes were expressed directly as active forms while the degradative enzymes were activated late by cAMP. In summary, the energy-metabolism oscillation is basically regulated by a feedback loop of oxido-reductive reactions of energy metabolism mediated by metabolites like NADH and ATP, and is modulated by metabolism of storage carbohydrates in combination of post-translational and transcriptional regulation of the related enzymes. A potential mechanism of energy-metabolism oscillation is proposed.

Interspecies interactions are an integral determinant of microbial community dynamics

PubMed Central

Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

2015-01-01

This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

Quantifying in situ growth rate of a filamentous bacterial species in activated sludge using rRNA:rDNA ratio.

PubMed

Nguyen, Vivi L; He, Xia; de Los Reyes, Francis L

2016-11-01

If the in situ growth rate of filamentous bacteria in activated sludge can be quantified, researchers can more accurately assess the effect of operating conditions on the growth of filaments and improve the mathematical modeling of filamentous bulking. We developed a method to quantify the in situ specific growth rate of Sphaerotilus natans (a model filament) in activated sludge using the species-specific 16S rRNA:rDNA ratio. Primers targeting the 16S rRNA of S. natans were designed, and real-time PCR and RT-PCR were used to quantify DNA and RNA levels of S. natans, respectively. A positive linear relationship was found between the rRNA:rDNA ratio (from 440 to 4500) and the specific growth rate of S. natans (from 0.036 to 0.172 h -1 ) using chemostat experiments. The in situ growth rates of S. natans in activated sludge samples from three water reclamation facilities were quantified, illustrating how the approach can be applied in a complex environment such as activated sludge. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Thermodynamic analysis of fermentation and anaerobic growth of baker's yeast for ethanol production.

PubMed

Teh, Kwee-Yan; Lutz, Andrew E

2010-05-17

Thermodynamic concepts have been used in the past to predict microbial growth yield. This may be the key consideration in many industrial biotechnology applications. It is not the case, however, in the context of ethanol fuel production. In this paper, we examine the thermodynamics of fermentation and concomitant growth of baker's yeast in continuous culture experiments under anaerobic, glucose-limited conditions, with emphasis on the yield and efficiency of bio-ethanol production. We find that anaerobic metabolism of yeast is very efficient; the process retains more than 90% of the maximum work that could be extracted from the growth medium supplied to the chemostat reactor. Yeast cells and other metabolic by-products are also formed, which reduces the glucose-to-ethanol conversion efficiency to less than 75%. Varying the specific ATP consumption rate, which is the fundamental parameter in this paper for modeling the energy demands of cell growth, shows the usual trade-off between ethanol production and biomass yield. The minimum ATP consumption rate required for synthesizing cell materials leads to biomass yield and Gibbs energy dissipation limits that are much more severe than those imposed by mass balance and thermodynamic equilibrium constraints. 2010 Elsevier B.V. All rights reserved.

A novel adaptive biogeochemical model, and its 3-D application for a decadal hindcast simulation of the biogeochemistry of the southern North Sea

NASA Astrophysics Data System (ADS)

Kerimoglu, Onur; Hofmeister, Richard; Wirtz, Kai

2016-04-01

Adaptation and acclimation processes are often ignored in ecosystem-scale model implementations, despite the long-standing recognition of their importance. Here we present a novel adaptive phytoplankton growth model where acclimation of the community to the changes in external resource ratios is accounted for, using optimality principles and dynamic physiological traits. We show that the model can reproduce the internal stoichiometries obtained at marginal supply ratios in chemostat experiments. The model is applied in a decadal hindcast simulation of the southern North Sea, where it is coupled to a 2-D benthic model and a 3-D hydrodynamic model in an approximately 1.5km horizontal resolution at the German Bight coast. The model is shown to have good skill in capturing the steep, coastal gradients in the German Bight, suggested by the match between the estimated and observed dissolved nutrient and chlorophyll concentrations. We then analyze the differential sensitivity of the coastal and off-shore zones to major drivers of the system, such as riverine nutrient loads. We demonstrate that the relevance of phytoplankton acclimation varies across coastal gradients and can become particularly significant in terms of summer nutrient depletion.

Competitive Abilities in Experimental Microcosms Are Accurately Predicted by a Demographic Index for R*

PubMed Central

Murrell, Ebony G.; Juliano, Steven A.

2012-01-01

Resource competition theory predicts that R*, the equilibrium resource amount yielding zero growth of a consumer population, should predict species' competitive abilities for that resource. This concept has been supported for unicellular organisms, but has not been well-tested for metazoans, probably due to the difficulty of raising experimental populations to equilibrium and measuring population growth rates for species with long or complex life cycles. We developed an index (Rindex) of R* based on demography of one insect cohort, growing from egg to adult in a non-equilibrium setting, and tested whether Rindex yielded accurate predictions of competitive abilities using mosquitoes as a model system. We estimated finite rate of increase (λ′) from demographic data for cohorts of three mosquito species raised with different detritus amounts, and estimated each species' Rindex using nonlinear regressions of λ′ vs. initial detritus amount. All three species' Rindex differed significantly, and accurately predicted competitive hierarchy of the species determined in simultaneous pairwise competition experiments. Our Rindex could provide estimates and rigorous statistical comparisons of competitive ability for organisms for which typical chemostat methods and equilibrium population conditions are impractical. PMID:22970128

The Two-Component System PhoPR of Clostridium acetobutylicum Is Involved in Phosphate-Dependent Gene Regulation ▿

PubMed Central

Fiedler, Tomas; Mix, Maren; Meyer, Uta; Mikkat, Stefan; Glocker, Michael O.; Bahl, Hubert; Fischer, Ralf-Jörg

2008-01-01

The phoPR gene locus of Clostridium acetobutylicum ATCC 824 comprises two genes, phoP and phoR. Deduced proteins are predicted to represent a response regulator and sensor kinase of a phosphate-dependent two-component regulatory system. We analyzed the expression patterns of phoPR in Pi-limited chemostat cultures and in response to Pi pulses. A basic transcription level under high-phosphate conditions was shown, and a significant increase in mRNA transcript levels was found when external Pi concentrations dropped below 0.3 mM. In two-dimensional gel electrophoresis experiments, a 2.5-fold increase in PhoP was observed under Pi-limiting growth conditions compared to growth with an excess of Pi. At least three different transcription start points for phoP were determined by primer extension analyses. Proteins PhoP and an N-terminally truncated *PhoR were individually expressed heterologously in Escherichia coli and purified. Autophosphorylation of *PhoR and phosphorylation of PhoP were shown in vitro. Electromobility shift assays proved that there was a specific binding of PhoP to the promoter region of the phosphate-regulated pst operon of C. acetobutylicum. PMID:18689481

A novel fermentation strategy for removing the key inhibitor acetic acid and efficiently utilizing the mixed sugars from lignocellulosic hydrolysates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mark A. Eiteman PHD; Elliot Altman Phd

2009-02-11

As part of preliminary research efforts, we have completed several experiments which demonstrate 'proof of concept.' These experiments addressed the following three questions: (1) Can a synthetic mixed sugar solution of glucose and xylose be efficiently consumed using the multi-organism approach? (2) Can this approach be used to accumulate a model product? (3) Can this approach be applied to the removal of an inhibitor, acetate, selectively from mixtures of xylose and glucose? To answer the question of whether this multi-organism approach can effectively consume synthetic mixed sugar solutions, we first tested substrate-selective uptake using two strains, one unable to consumemore » glucose and one unable to consume xylose. The xylose-selective strain ALS998 has mutations in the three genes involved in glucose uptake, rendering it unable to consume glucose: ptsG codes for the Enzyme IICB{sup Glc} of the phosphotransferase system (PTS) for carbohydrate transport (Postma et al., 1993), manZ codes for the IID{sup Man} domain of the mannose PTS permease (Huber, 1996), glk codes for glucokinase (Curtis and Epstein 1975) We also constructed strain ALS1008 which has a knockout in the xylA gene encoding for xylose isomerase, rendering ALS1008 unable to consume xylose. Two batch experiments and one continuous bioprocess were completed. In the first experiment, each strain was grown separately in a defined medium of 8 g/L xylose and 15 g/L glucose which represented xylose and glucose concentrations that can be generated by actual biomass. In the second experiment, the two strains were grown together in batch in the same defined, mixed-sugar medium. In a third experiment, we grew the strains continuously in a 'chemostat', except that we shifted the concentrations of glucose and xylose periodically to observe how the system would respond. (For example, we shifted the glucose concentration suddenly from 15 g/L to 30 g/L in the feed).« less

Monitoring and reactive-transport modeling of the spatial and temporal variations of the Strengbach spring hydrochemistry

NASA Astrophysics Data System (ADS)

Ackerer, J.; Chabaux, F.; Lucas, Y.; Clément, A.; Fritz, B.; Beaulieu, E.; Viville, D.; Pierret, M. C.; Gangloff, S.; Négrel, Ph.

2018-03-01

This study focuses on 20 years of hydrochemical monitoring of the small springs that emerge in the experimental granitic catchment of Strengbach (OHGE, France) and the simulation of these data using the KIRMAT code. The data indicate that the Strengbach springs display chemostatic behavior; that is, limited temporal variations were noted in the concentrations of dissolved silica (H4SiO4) and most of the basic cations during the studied period (1987-2010), resulting in relative stability of the global weathering fluxes exported by the springs. Only the Ca2+ concentrations reflect a significant decrease in all the Strengbach springs since 1987, and the variations differ from one spring to another. The modeling results show that the decrease in Ca2+ in the Strengbach springs is due to the response of the water-rock interactions within the bedrock to the variations in the chemical composition of the soil solutions, which were characterized by a significant increase in pH and a decrease in Ca2+ concentrations between 1987 and 2010. The decrease in Ca2+ concentrations seen in the Strengbach springs is controlled by changes in the apatite dissolution rate and the compositions of clay minerals induced by the soil solution changes. The differences observed between the Ca2+ trends of the springs are related to changes in the residence time of the water supplying the different springs. The weak impact of the soil solution modifications on the dissolution rates of other primary minerals and on the bulk precipitation rates of the clay minerals explains the relative stability over time of the concentrations of the other cations and dissolved silica in the water derived from the Strengbach springs. Further, the hydrochemical simulations suggest that the chemostatic behavior of the Strengbach springs cannot be explained by the mobilization of waters that are close to chemical equilibrium, but rather by a hydrological control of the spring water residence times. Finally, a comparison of current and long-term weathering rates determined from the spring water monitoring and a regolith profile shows that the modern chemical fluxes of Ca2+ are higher than the long-term ones, whereas the weathering fluxes of H4SiO4 and Na+ have likely been much more stable over time. All of these results indicate that the silicate weathering processes are characterized by weak spatial and temporal variability in the Strengbach catchment, while the chemical elements such as Ca2+, for which the budget in the spring waters is controlled by the dynamic behavior of clay minerals and minor minerals such as apatite, are significantly affected by Quaternary climatic variations and decennial environmental changes.

Overproduction of Threonine Aldolase Circumvents the Biosynthetic Role of Pyruvate Decarboxylase in Glucose-Limited Chemostat Cultures of Saccharomyces cerevisiae

PubMed Central

van Maris, Antonius J. A.; Luttik, Marijke A. H.; Winkler, Aaron A.; van Dijken, Johannes P.; Pronk, Jack T.

2003-01-01

Pyruvate decarboxylase-negative (Pdc−) mutants of Saccharomyces cerevisiae require small amounts of ethanol or acetate to sustain aerobic, glucose-limited growth. This nutritional requirement has been proposed to originate from (i) a need for cytosolic acetyl coenzyme A (acetyl-CoA) for lipid and lysine biosynthesis and (ii) an inability to export mitochondrial acetyl-CoA to the cytosol. To test this hypothesis and to eliminate the C2 requirement of Pdc− S. cerevisiae, we attempted to introduce an alternative pathway for the synthesis of cytosolic acetyl-CoA. The addition of l-carnitine to growth media did not restore growth of a Pdc− strain on glucose, indicating that the C2 requirement was not solely due to the inability of S. cerevisiae to synthesize this compound. The S. cerevisiae GLY1 gene encodes threonine aldolase (EC 4.1.2.5), which catalyzes the cleavage of threonine to glycine and acetaldehyde. Overexpression of GLY1 enabled a Pdc− strain to grow under conditions of carbon limitation in chemostat cultures on glucose as the sole carbon source, indicating that acetaldehyde formed by threonine aldolase served as a precursor for the synthesis of cytosolic acetyl-CoA. Fractionation studies revealed a cytosolic localization of threonine aldolase. The absence of glycine in these cultures indicates that all glycine produced by threonine aldolase was either dissimilated or assimilated. These results confirm the involvement of pyruvate decarboxylase in cytosolic acetyl-CoA synthesis. The Pdc− GLY1 overexpressing strain was still glucose sensitive with respect to growth in batch cultivations. Like any other Pdc− strain, it failed to grow on excess glucose in batch cultures and excreted pyruvate when transferred from glucose limitation to glucose excess. PMID:12676688

Molecular Detection, Isolation, and Physiological Characterization of Functionally Dominant Phenol-Degrading Bacteria in Activated Sludge

PubMed Central

Watanabe, Kazuya; Teramoto, Maki; Futamata, Hiroyuki; Harayama, Shigeaki

1998-01-01

DNA was isolated from phenol-digesting activated sludge, and partial fragments of the 16S ribosomal DNA (rDNA) and the gene encoding the largest subunit of multicomponent phenol hydroxylase (LmPH) were amplified by PCR. An analysis of the amplified fragments by temperature gradient gel electrophoresis (TGGE) demonstrated that two major 16S rDNA bands (bands R2 and R3) and two major LmPH gene bands (bands P2 and P3) appeared after the activated sludge became acclimated to phenol. The nucleotide sequences of these major bands were determined. In parallel, bacteria were isolated from the activated sludge by direct plating or by plating after enrichment either in batch cultures or in a chemostat culture. The bacteria isolated were classified into 27 distinct groups by a repetitive extragenic palindromic sequence PCR analysis. The partial nucleotide sequences of 16S rDNAs and LmPH genes of members of these 27 groups were then determined. A comparison of these nucleotide sequences with the sequences of the major TGGE bands indicated that the major bacterial populations, R2 and R3, possessed major LmPH genes P2 and P3, respectively. The dominant populations could be isolated either by direct plating or by chemostat culture enrichment but not by batch culture enrichment. One of the dominant strains (R3) which contained a novel type of LmPH (P3), was closely related to Valivorax paradoxus, and the result of a kinetic analysis of its phenol-oxygenating activity suggested that this strain was the principal phenol digester in the activated sludge. PMID:9797297

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

PubMed Central

Knijnenburg, Theo A; de Winde, Johannes H; Daran, Jean-Marc; Daran-Lapujade, Pascale; Pronk, Jack T; Reinders, Marcel JT; Wessels, Lodewyk FA

2007-01-01

Background Regulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the generated regulatory network, they are usually lacking. This is due to the fact that the large heterogeneity in the employed conditions and the continuous changes in environmental parameters in the often used shake-flask cultures, prevent the unambiguous modeling of the cultivation conditions within the computational framework. Results We designed an experimental setup that allows us to explicitly model the cultivation conditions and use these to infer the activity of TFs. The yeast Saccharomyces cerevisiae was cultivated under four different nutrient limitations in both aerobic and anaerobic chemostat cultures. In the chemostats, environmental and growth parameters are accurately controlled. Consequently, the measured transcriptional response can be directly correlated with changes in the limited nutrient or oxygen concentration. We devised a tailor-made computational approach that exploits the systematic setup of the cultivation conditions in order to identify the individual and combined effects of nutrient limitations and oxygen availability on expression behavior and TF activity. Conclusion Incorporating the actual growth conditions when inferring regulatory relationships provides detailed insight in the functionality of the TFs that are triggered by changes in the employed cultivation conditions. For example, our results confirm the established role of TF Hap4 in both aerobic regulation and glucose derepression. Among the numerous inferred condition-specific regulatory associations between gene sets and TFs, also many novel putative regulatory mechanisms, such as the possible role of Tye7 in sulfur metabolism, were identified. PMID:17241460

Exploiting combinatorial cultivation conditions to infer transcriptional regulation.

PubMed

Knijnenburg, Theo A; de Winde, Johannes H; Daran, Jean-Marc; Daran-Lapujade, Pascale; Pronk, Jack T; Reinders, Marcel J T; Wessels, Lodewyk F A

2007-01-22

Regulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the generated regulatory network, they are usually lacking. This is due to the fact that the large heterogeneity in the employed conditions and the continuous changes in environmental parameters in the often used shake-flask cultures, prevent the unambiguous modeling of the cultivation conditions within the computational framework. We designed an experimental setup that allows us to explicitly model the cultivation conditions and use these to infer the activity of TFs. The yeast Saccharomyces cerevisiae was cultivated under four different nutrient limitations in both aerobic and anaerobic chemostat cultures. In the chemostats, environmental and growth parameters are accurately controlled. Consequently, the measured transcriptional response can be directly correlated with changes in the limited nutrient or oxygen concentration. We devised a tailor-made computational approach that exploits the systematic setup of the cultivation conditions in order to identify the individual and combined effects of nutrient limitations and oxygen availability on expression behavior and TF activity. Incorporating the actual growth conditions when inferring regulatory relationships provides detailed insight in the functionality of the TFs that are triggered by changes in the employed cultivation conditions. For example, our results confirm the established role of TF Hap4 in both aerobic regulation and glucose derepression. Among the numerous inferred condition-specific regulatory associations between gene sets and TFs, also many novel putative regulatory mechanisms, such as the possible role of Tye7 in sulfur metabolism, were identified.

Responses and recovery assessment of continuously cultured Nitrosomonas europaea under chronic ZnO nanoparticle stress: Effects of dissolved oxygen.

PubMed

Wu, Junkang; Chang, Yan; Gao, Huan; Liang, Geyu; Yu, Ran; Ding, Zhen

2018-03-01

Although the antibacterial performances of emerging nanoparticles (NPs) have been extensively explored in the nitrifying systems, the impacts of dissolved oxygen (DO) levels on their bio-toxicities to the nitrifiers and the impaired cells' recovery potentials have seldom been addressed yet. In this study, the physiological and transcriptional responses of the typical ammonia oxidizers - Nitrosomonas europaea in a chemostat to the chronic ZnO NP exposure under different DO conditions were investigated. The results indicated that the cells in steady-growth state in the chemostat were more persevering than batch cultured ones to resist ZnO NP stress despite the dose-dependent NP inhibitory effects were observed. In addition, the occurred striking over-expressions of amoA and hao genes at the initial NP exposure stage suggested the cells' self-regulation potentials at the transcriptional level. The low DO (0.5 mg/L) cultured cells displayed higher sensitivity to NP stress than the high DO (2.0 mg/L) cultured ones, probably owning to the inefficient oxygen-dependent electron transfer from ammonia oxidation for energy conversion/production. The following 12-h NP-free batch recovery assays revealed that both high and low DO cultured cells possessed the physiological and metabolic activity recovery potentials, which were in negative correlation with the NP exposure time. The duration of NP stress and the resulting NP dissolution were critical for the cells' damage levels and their performance recoverability. The membrane preservation processes and the associated metabolism regulations were expected to actively participate in the cells' self-adaption to NP stress and thus be responsible for their metabolic activities recovery. Copyright © 2017 Elsevier Ltd. All rights reserved.

In situ expression of nifD in Geobacteraceae in subsurface sediments

USGS Publications Warehouse

Holmes, Dawn E.; Nevin, Kelly P.; Lovely, Derek R.

2004-01-01

In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 μM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.

Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate.

PubMed

Srivastava, Shaili; Bharti, Randhir K; Thakur, Indu Shekhar

2015-01-01

Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO3 respectively. These six isolates were tested for sequestration of carbon dioxide by (14)C metabolic labeling of NaH(14)CO3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH(14)CO3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm(-1). Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.

Mutational analysis of the hyc-operon determining the relationship between hydrogenase-3 and NADH pathway in Enterobacter aerogenes.

PubMed

Pi, Jian; Jawed, Muhammad; Wang, Jun; Xu, Li; Yan, Yunjun

2016-01-01

In this study, the hydrogenase-3 gene cluster (hycDEFGH) was isolated and identified from Enterobacter aerogenes CCTCC AB91102. All gene products were highly homologous to the reported bacterial hydrogenase-3 (Hyd-3) proteins. The genes hycE, hycF, hycG encoding the subunits of hydrogenase-3 were targeted for genetic knockout to inhibit the FHL hydrogen production pathway via the Red recombination system, generating three mutant strains AB91102-E (ΔhycE), AB91102-F (ΔhycF) and AB91102-G (ΔhycG). Deletion of the three genes affected the integrity of hydrogenase-3. The hydrogen production experiments with the mutant strains showed that no hydrogen was detected compared with the wild type (0.886 mol/mol glucose), demonstrating that knocking out any of the three genes could inhibit NADH hydrogen production pathway. Meanwhile, the metabolites of the mutant strains were significantly changed in comparison with the wild type, indicating corresponding changes in metabolic flux by mutation. Additionally, the activity of NADH-mediated hydrogenase was found to be nil in the mutant strains. The chemostat experiments showed that the NADH/NAD(+) ratio of the mutant strains increased nearly 1.4-fold compared with the wild type. The NADH-mediated hydrogenase activity and NADH/NAD(+) ratio analysis both suggested that NADH pathway required the involvement of the electron transport chain of hydrogenase-3. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization of two ammonia-oxidizing bacteria isolated from reactors operated with low dissolved oxygen concentrations.

PubMed

Park, H-D; Noguera, D R

2007-05-01

To obtain ammonia-oxidizing bacterial (AOB) strains inhabiting low dissolved oxygen (DO) environments and to characterize them to better understand their function and ecology. Using a serial dilution method, two AOB strains (ML1 and NL7) were isolated from chemostat reactors operated with low DO concentrations (0.12-0.24 mg l(-1)). Phylogenetically, strains ML1 and NL7 are affiliated to AOB within the Nitrosomonas europaea and Nitrosomonas oligotropha lineages, respectively. Kinetically, strain ML1 had high affinity for oxygen (0.24 +/- 0.13 mg l(-1)) and low affinity for ammonia (1.62 +/- 0.97 mg N l(-1)), while strain NL7 had high affinity for ammonia (0.48 +/- 0.35 mg l(-1)), but a surprisingly low affinity for oxygen (1.22 +/- 0.43 mg l(-1)). A co-culture experiment was used to iteratively estimate decay constants for both strains. The results indicated that AOB without high affinity for oxygen may have other mechanisms to persist in low DO environments, with high affinity for ammonia being important. This study provides a method to determine AOB growth kinetic parameters without assuming or neglecting decay constant. And, this is the first report on oxygen affinity constant of a N. oligotropha strain.

[MODIS Investigation

NASA Technical Reports Server (NTRS)

Abbott, Mark R.

1998-01-01

The objectives of the last six months were: Continue analysis of Hawaii Ocean Time-series (HOT) bio-optical mooring data, Recover instrumentation from JGOFS cruises in the Southern Ocean and analyze data Maintain documentation of MOCEAN algorithms and software for use by MOCEAN and GLI teams Continue chemostat experiments on the relationship of fluorescence quantum yield to environmental factors. Continue to develop and expand browser-based information system for in situ bio-optical data Work Analysis of Field Data from Hawaii We are continuing to analyze bio-optical data collected at the Hawaii Ocean Time Series mooring. The HOT bio-optical mooring was recovered in May 1998. After retrieving the data, the sensor package was serviced and redeployed. We now have over 18 months of data. These are being analyzed as part of a larger study of mesoscale processes at this JGOFS time series site. We have had some failures in the data logger which have affected the fluorescence channels. These are being repaired. We also had an instrument housing failure, and minor modifications have been made to avoid subsequent problems. In addition, Ricardo Letelier is funded as part of the SeaWiFS calibrator/validation effort (through a subcontract from the University of Hawaii, Dr. John Porter), and he is collecting bio-optical and fluorescence data as part of the HOT activity.

Final Report: Connecting genomic capabilities to physiology and response: Systems biology of the widespread alga Micromonas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Worden, Alexandra Z.; Callister, Stephen; Stuart, Joshua

Increased stratification, less mixing and reduced nutrient concentrations in marine surface waters are predicted under a number of climate-change scenarios. These conditions are considered favorable for tiny photosynthetic algae (picophytoplankton), shaping their role in mediating future CO2 conditions. One possibility is that picophytoplankton such as Micromonas that have broad geographical ranges will more successfully adapt to changing environmental conditions. However, their capacity to thrive under the multi-factorial impacts of low pH, low nutrients, increasing temperature and changes in community composition is not known. Here, we developed the dual-Micromonas model system, which entailed generating optimized genomic information for two Micromonas speciesmore » and developing a highperformance chemostat system in which both CO2 and nutrients could be consistently manipulated. This system is now fully operational. Project results are available in several publications will others are still in the analysis phase. Overall, our results show that Micromonas primary production will likely decrease under predicted future climate conditions. Furthermore, our studies on Micromonas provide new insights to the land plant ancestor, including the discovery of conserved signaling mechanisms (known to be essential to plant development) as well as the discovery of widespread chemical-sensing molecular switches. Collectively, this research highlights Micromonas as an important new model green alga for understanding plant gene networks and evolution as well as for investigating perturbation effects on marine primary production.« less

Amino Acid Isotopic Trophic Enrichment in Mesozooplankton: Is Alanine a Better Predictor of Protistan Grazer Steps?

NASA Astrophysics Data System (ADS)

Decima, M.; Landry, M. R.; Bradley, C. J.; Fogel, M. L.

2016-02-01

Food-web studies within marine environments are increasingly reliant upon results from compound-specific isotope analysis of amino acids (CSIA-AA). The approach is advantageous because it allows consumer trophic positions to be estimated without sampling the dynamic primary producers. The baseline signal in the source AA phenylalanine is preserved, and a constant enrichment in glutamic acid at each trophic step is assumed, regardless of consumer type or diet. However, a number of recent studies challenge the assumption of universal and invariant isotopic fractionation of glutamic acid for all trophic levels, as well as its specific applicability to the main grazers in the ocean: the protistan microzooplankton. We present results from both laboratory and field studies that further explore this issue. Experiments include six 2-stage chemostats, using two different microzooplankton-phytoplankton pairs and one copepod-phytoplankton pair, and one 3-stage experiment using a copepod-microzooplankton-phytoplankton chain. We confirm previous observations of negligible fractionation of glutamic acid in protistan consumers when nutrients are limiting. In contrast, a consistent trophic enrichment effect was observed for alanine, with increasing δ15N values by trophic level for both metazoan and protistan consumers. A re-analysis of published CSIA-AA data of zooplankton species show that an index using alanine and phenylalanine gives trophic level estimates closer to expected given current understanding of the linkages within microbial food webs. Our results examine the details of isotopic fractionation of alanine within defined food chains and generally support its potential use as a trophic level indicator that includes the protistan contribution to mesozooplankton diet.

Concentration-discharge relationships under the microscope: high frequency measurement in rivers

NASA Astrophysics Data System (ADS)

Floury, P.; Gaillardet, J.; Bouchez, J.; Tallec, G.; Gayer, E.; Ansart, P.; Blanchouin, A.

2017-12-01

Concentration-discharge relationships (C-Q) of river water is a powerful tool to track the coupling between water flow and chemical reactions in the Critical Zone. C-Q have been extensively studied the last two decades. We present a new C-Q data series recorded at 40-minutes frequency by a prototype called River Lab (RL) (Floury et al., 2017). Confined in a bungalow next to the river, the RL performs an of all major dissolved species (Na+, K+, Mg2+, Ca2+, Cl-, SO42-, NO3-) using ion chromatographs, through continuous sampling and filtration of the river water. The RL was deployed in 2015 in the Orgeval hydrological Observatory (OZCAR French Research Infrastructure), an agricultural watershed underlain by carbonates, France. We present five major flood events recorded over one hydrological year. We present the C-Q for each of the flood events. We observe i) element-specific C-Q ii) C-Q loops, the size and the excentricity of which decrease with the intensity of the flood. The most reproducible C-Q patterns are observed for Na+, Mg2+, Ca2+, Cl-, SO42-, whereas K+ and NO3- present a more erratic behaviour. We discuss the chemostatic behaviour of species concentrations using a fitting by a power law function. It is likely that C-Q will depend on the time during a single flood event and also over the year. The chemostatic behaviour of each species change over the year and also during a single flood event. We focus our interpretations on the recession of each flood event, where precipitation and evapotrapiration can be considered as negligible. We propose a "grey box" aproach such as already developed from stream flow (Kirchner, 2009) but here extended to solute fluxes. Floury et al. Hydrol. Earth Syst. Sci. Discuss., doi:10.5194/hess-2017-12, 2017. Kirchner. Water Ressources Research, VOL. 45, W02429, doi:10.1029/2008WR006912, 2009.

Oxygen-Dependent Growth of the Sulfate-Reducing Bacterium Desulfovibrio oxyclinae in Coculture with Marinobacter sp. Strain MB in an Aerated Sulfate-Depleted Chemostat

PubMed Central

Sigalevich, Pavel; Cohen, Yehuda

2000-01-01

A chemostat coculture of the sulfate-reducing bacterium Desulfovibrio oxyclinae and the facultatively aerobic heterotroph Marinobacter sp. strain MB was grown for 1 week under anaerobic conditions at a dilution rate of 0.05 h−1. It was then exposed to an oxygen flux of 223 μmol min−1 by gassing the growth vessel with 5% O2. Sulfate reduction persisted under these conditions, though the amount of sulfate reduced decreased by 45% compared to the amount reduced during the initial anaerobic mode. After 1 week of growth under these conditions, sulfate was excluded from the incoming medium. The sulfate concentration in the growth vessel decreased exponentially from 4.1 mM to 2.5 μM. The coculture consumed oxygen effectively, and no residual oxygen was detected during either growth mode in which oxygen was supplied. The proportion of D. oxyclinae cells in the coculture as determined by in situ hybridization decreased from 86% under anaerobic conditions to 70% in the microaerobic sulfate-reducing mode and 34% in the microaerobic sulfate-depleted mode. As determined by the most-probable-number (MPN) method, the numbers of viable D. oxyclinae cells during the two microaerobic growth modes decreased compared to the numbers during the anaerobic growth mode. However, there was no significant difference between the MPN values for the two modes when oxygen was supplied. The patterns of consumption of electron donors and acceptors suggested that when oxygen was supplied in the absence of sulfate and thiosulfate, D. oxyclinae performed incomplete aerobic oxidation of lactate to acetate. This is the first observation of oxygen-dependent growth of a sulfate-reducing bacterium in the absence of either sulfate or thiosulfate. Cells harvested during the microaerobic sulfate-depleted stage and exposed to sulfate and thiosulfate in a respiration chamber were capable of anaerobic sulfate and thiosulfate reduction. PMID:11055958

Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

PubMed Central

Li, Fangting

2017-01-01

The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent landscape perspective permits a quantitative discussion of a wide range of biological phenomena as nonlinear, stochastic dynamics. PMID:28490602

Influence of Different Electron Donors and Acceptors on Dehalorespiration of Tetrachloroethene by Desulfitobacterium frappieri TCE1

PubMed Central

Gerritse, Jan; Drzyzga, Oliver; Kloetstra, Geert; Keijmel, Mischa; Wiersum, Luit P.; Hutson, Roger; Collins, Matthew D.; Gottschal, Jan C.

1999-01-01

Strain TCE1, a strictly anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE), was isolated by selective enrichment from a PCE-dechlorinating chemostat mixed culture. Strain TCE1 is a gram-positive, motile, curved rod-shaped organism that is 2 to 4 by 0.6 to 0.8 μm and has approximately six lateral flagella. The pH and temperature optima for growth are 7.2 and 35°C, respectively. On the basis of a comparative 16S rRNA sequence analysis, this bacterium was identified as a new strain of Desulfitobacterium frappieri, because it exhibited 99.7% relatedness to the D. frappieri type strain, strain PCP-1. Growth with H2, formate, l-lactate, butyrate, crotonate, or ethanol as the electron donor depends on the availability of an external electron acceptor. Pyruvate and serine can also be used fermentatively. Electron donors (except formate and H2) are oxidized to acetate and CO2. When l-lactate is the growth substrate, strain TCE1 can use the following electron acceptors: PCE and TCE (to produce cis-1,2-dichloroethene), sulfite and thiosulfate (to produce sulfide), nitrate (to produce nitrite), and fumarate (to produce succinate). Strain TCE1 is not able to reductively dechlorinate 3-chloro-4-hydroxyphenylacetate. The growth yields of the newly isolated bacterium when PCE is the electron acceptor are similar to those obtained for other dehalorespiring anaerobes (e.g., Desulfitobacterium sp. strain PCE1 and Desulfitobacterium hafniense) and the maximum specific reductive dechlorination rates are 4 to 16 times higher (up to 1.4 μmol of chloride released · min−1 · mg of protein−1). Dechlorination of PCE and TCE is an inducible process. In PCE-limited chemostat cultures of strain TCE1, dechlorination is strongly inhibited by sulfite but not by other alternative electron acceptors, such as fumarate or nitrate. PMID:10583967

Transport by the lactose permease of Escherichia coli as the basis of lactose killing.

PubMed Central

Dykhuizen, D; Hartl, D

1978-01-01

Lactose killing is a peculiar phenomenon in which 80 to 98% of the Escherichia coli cells taken from a lactose-limited chemostat die when plated on standard lactose minimal media. This unique form of suicide is caused by the action of the lactose permease. Since uptake of either lactose or galactose by the lactose permease caused death, the action of rapid transport across the membrane must be the cause of the phenomenon. Alternative causes of lactose killing, such as accumulation of toxic metabolic intermediates or action of the beta-galactosidase, have been eliminated. It is proposed that rapid uptake of sugars by the lactose permease disrupts membrane function, perhaps causing collapse of the membrane potential. PMID:99437

Multimodal Microchannel and Nanowell-Based Microfluidic Platforms for Bioimaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, Tao; Smallwood, Chuck R.; Zhu, Ying

2017-03-30

Modern live-cell imaging approaches permit real-time visualization of biological processes. However, limitations for unicellular organism trapping, culturing and long-term imaging can preclude complete understanding of how such microorganisms respond to perturbations in their local environment or linking single-cell variability to whole population dynamics. We have developed microfluidic platforms to overcome prior technical bottlenecks to allow both chemostat and compartmentalized cellular growth conditions using the same device. Additionally, a nanowell-based platform enables a high throughput approach to scale up compartmentalized imaging optimized within the microfluidic device. These channel and nanowell platforms are complementary, and both provide fine control over the localmore » environment as well as the ability to add/replace media components at any experimental time point.« less

Selection of mutants tolerant of oxidative stress from respiratory cultures of Lactobacillus plantarum C17.

PubMed

Zotta, T; Ianniello, R G; Guidone, A; Parente, E; Ricciardi, A

2014-03-01

Lactobacillus plantarum is a lactic acid bacterium involved in the production of many fermented foods. Recently, several studies have demonstrated that aerobic or respiratory metabolism in this species leads to improved technological and stress response properties. We investigated respiratory growth, metabolite production and stress resistance of Lact. plantarum C17 during batch, fed-batch and chemostat cultivations under respiratory conditions. Sixty mutants were selected for their ability to tolerate oxidative stress using H2 O2 and menadione as selective agents and further screened for their capability to growth under anaerobic, respiratory and oxidative stress conditions. Dilution rate clearly affected the physiological state of cells and, generally, slow-growing cultures had improved survival to stresses, catalase production and oxygen uptake. Most mutants were more competitive in terms of biomass production and ROS degradation compared with wild-type strain (wt) C17 and two of these (C17-m19 and C17-m58) were selected for further experiments. This work confirms that, in Lact. plantarum, respiration and low growth rates confer physiological and metabolic advantages compared with anaerobic cultivation. Our strategy of natural selection successfully provides a rapid and inexpensive screening for a large number of strains and represents a food-grade approach of practical relevance in the production of starter and probiotic cultures. © 2013 The Society for Applied Microbiology.

Proteome analysis of the Escherichia coli heat shock response under steady-state conditions

PubMed Central

Lüders, Svenja; Fallet, Claas; Franco-Lara, Ezequiel

2009-01-01

In this study a proteomic approach was used to investigate the steady-state response of Escherichia coli to temperature up-shifts in a cascade of two continuously operated bioreactors. The first reactor served as cell source with optimal settings for microbial growth, while in the second chemostat the cells were exposed to elevated temperatures. By using this reactor configuration, which has not been reported to be used for the study of bacterial stress responses so far, it is possible to study temperature stress under well-defined, steady-state conditions. Specifically the effect on the cellular adaption to temperature stress using two-dimensional gel electrophoresis was examined and compared at the cultivation temperatures of 37°C and 47.5°C. As expected, the steady-state study with the double bioreactor configuration delivered a different protein spectrum compared to that obtained with standard batch experiments in shaking flasks and bioreactors. Setting a high cut-out spot-to-spot size ratio of 5, proteins involved in defence against oxygen stress, functional cell envelope proteins, chaperones and proteins involved in protein biosynthesis, the energy metabolism and the amino acid biosynthesis were found to be differently expressed at high cultivation temperatures. The results demonstrate the complexity of the stress response in a steady-state culture not reported elsewhere to date. PMID:19772559

Kinetic and microbiological characterization of aerobic granules performing partial nitritation of a low-strength wastewater at 10 °C.

PubMed

Reino, Clara; Suárez-Ojeda, María Eugenia; Pérez, Julio; Carrera, Julián

2016-09-15

A granular airlift reactor enriched in ammonia oxidizing bacteria (AOB) was operated at 10 °C performing stable partial nitritation in the long-term. The reactor treated a synthetic low-strength influent during 250 days with an average nitrogen loading rate of 0.63 ± 0.06 g N L(-1) d(-1). Nitrate production was barely detected, being the average concentration in the effluent of 0.6 ± 0.3 mg N-NO3 L(-1). Furthermore, a suitable effluent for a subsequent reactor performing the anammox process was achieved. A maximum specific growth rate as high as 0.63 ± 0.05 d(-1) was determined by performing kinetic experiments with the granular sludge in a chemostat and fitting the results to the Monod model. Pyrosequencing analysis showed a high enrichment in AOB (41 and 65% of the population were identified as Nitrosomonas genus on day 98 and 233, respectively) and an effective repression of nitrite oxidizing bacteria in the long-term. Pyrosequencing analysis also identified the coexistence of nitrifying bacteria and heterotrophic psychrotolerant microorganisms in the granular sludge. Some psychrotolerant microorganisms are producers of cryoprotective extracellular polymeric substances that could explain the better survival of the whole consortia at cold temperatures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cultivation of Aquincola tertiaricarbonis L108 on the fuel oxygenate intermediate tert-butyl alcohol induces aerobic anoxygenic photosynthesis at extremely low feeding rates.

PubMed

Rohwerder, Thore; Müller, Roland H; Weichler, M Teresa; Schuster, Judith; Hübschmann, Thomas; Müller, Susann; Harms, Hauke

2013-10-01

Aerobic anoxygenic photosynthesis (AAP) is found in an increasing number of proteobacterial strains thriving in ecosystems ranging from extremely oligotrophic to eutrophic. Here, we have investigated whether the fuel oxygenate-degrading betaproteobacterium Aquincola tertiaricarbonis L108 can use AAP to compensate kinetic limitations at low heterotrophic substrate fluxes. In a fermenter experiment with complete biomass retention and also during chemostat cultivation, strain L108 was challenged with extremely low substrate feeding rates of tert-butyl alcohol (TBA), an intermediate of methyl tert-butyl ether (MTBE). Interestingly, formation of photosynthetic pigments, identified as bacteriochlorophyll a and spirilloxanthin, was only induced in growing cells at TBA feeding rates less than or equal to maintenance requirements observed under energy excess conditions. Growth continued at rates between 0.001 and 0.002 h(-1) even when the TBA feed was decreased to values close to 30 % of this maintenance rate. Partial sequencing of genomic DNA of strain L108 revealed a bacteriochlorophyll synthesis gene cluster (bchFNBHL) and photosynthesis regulator genes (ppsR and ppaA) typically found in AAP and other photosynthetic proteobacteria. The usage of light as auxiliary energy source enabling evolution of efficient degradation pathways for kinetically limited heterotrophic substrates and for lowering the threshold substrate concentration Smin at which growth becomes zero is discussed.

Transformation of carbon tetrachloride and chloroform by trichloroethene respiring anaerobic mixed cultures and supernatant.

PubMed

Vickstrom, Kyle E; Azizian, Mohammad F; Semprini, Lewis

2017-09-01

Carbon tetrachloride (CT) and chloroform (CF) were transformed in batch reactor experiments conducted with anaerobic dechlorinating cultures and supernatant (ADC + S) harvested from continuous flow reactors. The Evanite (EV) and Victoria/Stanford (VS) cultures, capable of respiring trichloroethene (TCE), 1,2-cis-dichloroethene (cDCE), and vinyl chloride (VC) to ethene (ETH), were grown in continuous flow reactors receiving an influent feed of saturated TCE (10 mM; 60 mEq) and formate (45 mM; 90 mEq) but no CT or CF. Cells and supernatant were harvested from the chemostats and inoculated into batch reactors at the onset of each experiment. CT transformation was complete following first order kinetics with CF, DCM and CS 2 as the measurable transformation products, representing 20-40% of the original mass of CT, with CO 2 likely the unknown transformation product. CF was transformed to DCM and likely CO 2 at an order of magnitude rate lower than CT, while DCM was not further transformed. An analytical first order model including multiple key reactions effectively simulated CT transformation, product formation and transformation, and provided reasonable estimates of transformation rate coefficients. Biotic and abiotic treatments indicated that CT was mainly transformed via abiotic processes. However, the presence of live cells was associated with the transformation of CF to DCM. In biotic tests both TCE and CT were simultaneously transformed, with TCE transformed to ETH and approximately 15-53% less CF formed via CT transformation. A 14-day exposure to CF (CF max  = 1.4 μM) reduced all rates of chlorinated ethene respiration by a factor of 10 or greater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reactive transport model of growth and methane production by high-temperature methanogens in hydrothermal regions of the subseafloor

NASA Astrophysics Data System (ADS)

Stewart, L. C.; Algar, C. K.; Topçuoğlu, B. D.; Fortunato, C. S.; Larson, B. I.; Proskurowski, G. K.; Butterfield, D. A.; Vallino, J. J.; Huber, J. A.; Holden, J. F.

2014-12-01

Hydrogenotrophic methanogens are keystone high-temperature autotrophs in deep-sea hydrothermal vents and tracers of habitability and biogeochemical activity in the hydrothermally active subseafloor. At Axial Seamount, nearly all thermophilic methanogens are Methanothermococcus and Methanocaldococcus species, making this site amenable to modeling through pure culture laboratory experiments coupled with field studies. Based on field microcosm incubations with 1.2 mM, 20 μM, or no hydrogen, the growth of methanogens at 55°C and 80°C is limited primarily by temperature and hydrogen availability, with ammonium amendment showing no consistent effect on total methane output. The Arrhenius constants for methane production by Methanocaldococcus jannaschii (optimum 82°C) and Methanothermococcus thermolithotrophicus (optimum 65°C) were determined in pure culture bottle experiments. The Monod constants for hydrogen concentration were measured by growing both organisms in a 2-liter chemostat at two dilution rates; 55°C, 65°C and 82°C; and variable hydrogen concentrations. M. jannaschii showed higher ks and Vmax constants than M. thermolithotrophicus. In the field, hydrogen and methane concentrations in hydrothermal end-member and low-temperature diffuse fluids were measured, and the concentrations of methanogens that grow at 55°C and 80°C in diffuse fluids were determined using most-probable-number estimates. Methane concentration anomalies in diffuse fluids relative to end-member hydrothermal concentrations and methanogen cell concentrations are being used to constrain a 1-D reactive transport model using the laboratory-determined Arrhenius and Monod constants for methane production by these organisms. By varying flow path length and subseafloor cell concentrations in the model, our goal is to determine solutions for the potential depth of the subseafloor biosphere coupled with the amount of methanogenic biomass it contains.

Noise in gene expression is coupled to growth rate.

PubMed

Keren, Leeat; van Dijk, David; Weingarten-Gabbay, Shira; Davidi, Dan; Jona, Ghil; Weinberger, Adina; Milo, Ron; Segal, Eran

2015-12-01

Genetically identical cells exposed to the same environment display variability in gene expression (noise), with important consequences for the fidelity of cellular regulation and biological function. Although population average gene expression is tightly coupled to growth rate, the effects of changes in environmental conditions on expression variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most promoters, regardless of their specific expression values. We present a simple model of noise in expression that results from having an asynchronous population, with cells at different cell-cycle stages, and with different partitioning of the cells between the stages at different growth rates. This model predicts non-monotonic global changes in noise at different growth rates as well as overall higher variability in expression for cell-cycle-regulated genes in all conditions. The consistency between this model and our data, as well as with noise measurements of cells growing in a chemostat at well-defined growth rates, suggests that cell-cycle heterogeneity is a major contributor to gene expression noise. Finally, we identify gene and promoter features that play a role in gene expression noise across conditions. Our results show the existence of growth-related global changes in gene expression noise and suggest their potential phenotypic implications. © 2015 Keren et al.; Published by Cold Spring Harbor Laboratory Press.

Noise in gene expression is coupled to growth rate

PubMed Central

Keren, Leeat; van Dijk, David; Weingarten-Gabbay, Shira; Davidi, Dan; Jona, Ghil; Weinberger, Adina; Milo, Ron; Segal, Eran

2015-01-01

Genetically identical cells exposed to the same environment display variability in gene expression (noise), with important consequences for the fidelity of cellular regulation and biological function. Although population average gene expression is tightly coupled to growth rate, the effects of changes in environmental conditions on expression variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most promoters, regardless of their specific expression values. We present a simple model of noise in expression that results from having an asynchronous population, with cells at different cell-cycle stages, and with different partitioning of the cells between the stages at different growth rates. This model predicts non-monotonic global changes in noise at different growth rates as well as overall higher variability in expression for cell-cycle–regulated genes in all conditions. The consistency between this model and our data, as well as with noise measurements of cells growing in a chemostat at well-defined growth rates, suggests that cell-cycle heterogeneity is a major contributor to gene expression noise. Finally, we identify gene and promoter features that play a role in gene expression noise across conditions. Our results show the existence of growth-related global changes in gene expression noise and suggest their potential phenotypic implications. PMID:26355006

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

PubMed Central

Sunshine, Anna B.; Payen, Celia; Ong, Giang T.; Liachko, Ivan; Tan, Kean Ming; Dunham, Maitreya J.

2015-01-01

Aneuploidy is a hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains, each containing a different telomeric amplicon (Tamp), ranging in size from 0.4 to 1,000 kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific, with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome-wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp’s fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations. PMID:26011532

Population aging through survival of the fit and stable

NASA Astrophysics Data System (ADS)

Brotto, Tommaso; Bunin, Guy; Kurchan, Jorge

2016-03-01

Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates. Individuals reproduce and die with a rate that is a property of each state, not necessarily related to its stability, and the offspring is born on the parent’s state. The total population is limited by resources or space, as for example in a chemostat or a Petri dish. Our aim is to show that mutation rate and fitness become more correlated, even if they are completely uncorrelated for an isolated individual, underlining the fact that the interaction induced by limitation of resources is by itself efficient for generating collective effects.

Population control in symbiotic corals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Falkowski, P.G.; Dubinsky, Z.; Muscatine, L.

1993-10-01

Stability in symbiotic association requires control of population growth between symbionts. The population density of zooxanthellae per unit surface area of most symbiotic corals is remarkably consistant. How is the population density of zooxanthellae maintained and what happens to the symbiotic association if the balance between algae and host is perturbed. The answers to these question, examined in this paper, provide a framework for understanding how the size of the component populations is controlled in symbiotic associations. The topic areas covered include the following: carbon economy in a symbiotic coral; effects of nutrient enrichment; the chemostat model of population control;more » the effects of exposure to ammonium levels. Ammonium ions and organic materials are the factors which maintain the density of zooxanthellae. 32 refs., 5 figs.« less

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns.

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Cieplak, Marek; Maritan, Amos; Fedoroff, Nina V

2006-12-12

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems.

Evolution of concentration-discharge relations revealed by high frequency diurnal sampling of stream water during spring snowmelt

NASA Astrophysics Data System (ADS)

Olshansky, Y.; White, A. M.; Thompson, M.; Moravec, B. G.; McIntosh, J. C.; Chorover, J.

2017-12-01

Concentration discharge (C-Q) relations contain potentially important information on critical zone (CZ) processes including: weathering reactions, water flow paths and nutrient export. To examine the C-Q relations in a small (3.3 km2) headwater catchment - La Jara Creek located in the Jemez River Basin Critical Zone Observatory, daily, diurnal stream water samples were collected during spring snow melt 2017, from two flumes located in outlets of the La Jara Creek and a high elevation zero order basin within this catchment. Previous studies from this site (McIntosh et al., 2017) suggested that high frequency sampling was needed to improve our interpretation of C-Q relations. The dense sampling covered two ascending and two descending limbs of the snowmelt hydrograph, from March 1 to May 15, 2017. While Na showed inverse correlation (dilution) with discharge, most other solutes (K, Mg, Fe, Al, dissolved organic carbon) exhibited positive (concentration) or chemostatic trends (Ca, Mn, Si, dissolved inorganic carbon and dissolved nitrogen). Hysteresis in the C-Q relation was most pronounced for bio-cycled cations (K, Mg) and for Fe, which exhibited concentration during the first ascending limb followed by a chemostatic trend. A pulsed increase in Si concentration immediately after the first ascending limb in both flumes suggests mixing of deep groundwater with surface water. A continual increase in Ge/Si concentrations followed by a rapid decrease after the second rising limb may suggest a fast transition between soil water to ground water dominating the stream flow. Fourier transform infrared spectroscopy of selected samples across the hydrograph demonstrated pronounced changes in dissolved organic matter molecular composition with the advancement of the spring snow melt. X-ray micro-spectroscopy of colloidal material isolated from the collected water samples indicated a significant role for organic matter in the transport of inorganic colloids. Analyses of high frequency diurnal sampling greatly improve our ability to probe rapid CZ changes occurring during spring snowmelt, and provide useful information for evaluation and modeling of CZ processes in other snow melt dominated regions.

Simultaneous remediation of nutrients from liquid anaerobic digestate and municipal wastewater by the microalga Scenedesmus sp. AMDD grown in continuous chemostats.

PubMed

Dickinson, K E; Bjornsson, W J; Garrison, L L; Whitney, C G; Park, K C; Banskota, A H; McGinn, P J

2015-01-01

The primary aim of this study was to investigate the capacity of a microalga, Scenedesmus sp. AMDD, to remediate nutrients from municipal wastewater, either as the sole nutrient source or after blending with wastewater obtained from the anaerobic digestion of swine manure. A complimentary aim was to study and define the effects of these wastewaters on microalgal growth, biomass productivity and composition which have important implications for a commercial biofuels production system. A microalga, Scenedesmus sp. AMDD, was grown in continuous chemostats in municipal wastewater or wastewater supplemented with 1·6× or 2·4× higher levels of nitrogen (N) obtained through supplementation with anaerobic digestates. Biomass productivity increased with increasing nutrient supplementation, but was limited by light at high cell densities. Cellular quotas of carbon (C), nitrogen and phosphorus (P) all increased in direct proportion to their concentrations in the combined wastewaters. At higher cell densities, total carbohydrate decreased while protein increased. Fatty acid content remained relatively constant. Under high nutrient levels, the fatty acid profiles contained a higher concentration of polyunsaturated fatty acids at the expense of monounsaturated fatty acids. Chlorophyll a was 2·5 times greater in the treatment of greatest nutrient supplementation compared to the treatment with the least. Ammonium (NH4(+)) and phosphate (PO4(3-)) were completely removed by algal growth in all treatments and with maximal removal rates of 41·2 mg N l(-1) d(-1) and 6·7 mg P l(-1) d(-1) observed in wastewater amended with 2·4× higher N level. The study is the first to report stable, long-term continuous algal growth and productivity obtained by combining wastewaters of different sources. The study is supported by detailed analyses of the composition of the cultivated biomass and links composition to the nutrient and light availabilities in the cultures. Simultaneous remediation of these wastes by algal growth is discussed as a strategy for the valorization of the biomass. © 2014 Her Majesty the Queen in Right of Canada © 2014 The Society for Applied Microbiology. Reproduced with the permission of the Minister of Industry.

Coupling and uncoupling of triglyceride and beta-carotene production by Dunaliella salina under nitrogen limitation and starvation.

PubMed

Bonnefond, Hubert; Moelants, Nina; Talec, Amélie; Mayzaud, Patrick; Bernard, Olivier; Sciandra, Antoine

2017-01-01

Nitrogen starvation and limitation are known to induce important physiological changes especially in lipid metabolism of microalgae (triglycerides, membrane lipids, beta-carotene, etc.). Although little information is available for Dunaliella salina , it is a promising microalga for biofuel production and biotechnological applications due to its ability to accumulate lipid together with beta-carotene. Batch and chemostat experiments with various degrees of nitrogen limitation, ranging from starvation to nitrogen-replete conditions, were carried out to study carbon storage dynamics (total carbon, lipids, and beta-carotene) in steady state cultures of D. salina . A new protocol was developed in order to manage the very high beta-carotene concentrations and to more accurately separate and quantify beta-carotene and triglycerides by chromatography. Biomass evolution was appropriately described by the Droop model on the basis of the nitrogen quota dynamics. Triglycerides and beta-carotene were both strongly anti-correlated with nitrogen quota highlighting their carbon sink function in nitrogen depletion conditions. Moreover, these two valuable molecules were correlated each other for nitrogen replete conditions or moderated nitrogen limitations (N:C ratio higher than 0.04). Under nitrogen starvation, i.e., for very low N:C ratio, the dynamic revealed, for the first time, uncoupled part (higher triglyceride accumulation than beta-carotene), possibly because of shortage in key proteins involved in the stabilization of lipid droplets. This study motivates the accurate control of the microalgal nitrogen quota in order to optimize lipid productivity.

Process and reactor design for biophotolytic hydrogen production.

PubMed

Tamburic, Bojan; Dechatiwongse, Pongsathorn; Zemichael, Fessehaye W; Maitland, Geoffrey C; Hellgardt, Klaus

2013-07-14

The green alga Chlamydomonas reinhardtii has the ability to produce molecular hydrogen (H2), a clean and renewable fuel, through the biophotolysis of water under sulphur-deprived anaerobic conditions. The aim of this study was to advance the development of a practical and scalable biophotolytic H2 production process. Experiments were carried out using a purpose-built flat-plate photobioreactor, designed to facilitate green algal H2 production at the laboratory scale and equipped with a membrane-inlet mass spectrometry system to accurately measure H2 production rates in real time. The nutrient control method of sulphur deprivation was used to achieve spontaneous H2 production following algal growth. Sulphur dilution and sulphur feed techniques were used to extend algal lifetime in order to increase the duration of H2 production. The sulphur dilution technique proved effective at encouraging cyclic H2 production, resulting in alternating Chlamydomonas reinhardtii recovery and H2 production stages. The sulphur feed technique enabled photobioreactor operation in chemostat mode, resulting in a small improvement in H2 production duration. A conceptual design for a large-scale photobioreactor was proposed based on these experimental results. This photobioreactor has the capacity to enable continuous and economical H2 and biomass production using green algae. The success of these complementary approaches demonstrate that engineering advances can lead to improvements in the scalability and affordability of biophotolytic H2 production, giving increased confidence that H2 can fulfil its potential as a sustainable fuel of the future.

A Reactive-Transport Model Describing Methanogen Growth and Methane Production in Diffuse Flow Vents at Axial Seamount

NASA Astrophysics Data System (ADS)

Algar, C. K.

2015-12-01

Hydrogenotrophic methanogenesis is an important mode of metabolism in deep-sea hydrothermal vents. Diffuse vent fluids often show a depletion in hydrogen with a corresponding increase in methane relative to pure-mixing of end member fluid and seawater, and genomic surveys show an enrichment in genetic sequences associated with known methanogens. However, because we cannot directly sample the subseafloor habitat where these organisms are living, constraining the size and activity of these populations remains a challenge and limits our ability to quantify the role they play in vent biogeochemistry. Reactive-transport modeling may provide a useful tool for approaching this problem. Here we present a reactive-transport model describing methane production along the flow-path of hydrothermal fluid from its high temperature end-member to diffuse venting at the seafloor. The model is set up to reflect conditions at several diffuse vents in the Axial Seamount. The model describes the growth of the two dominant thermophilic methanogens, Methanothermococcus and Methanocaldococcus, observed at Axial seamount. Monod and Arrhenius constants for Methanothermococcus thermolithotrophicus and Methanocaldococcus jannaschii were obtained for the model using chemostat and bottle experiments at varying temperatures. The model is used to investigate the influence of different mixing regimes on the subseafloor populations of these methanogens. By varying the model flow path length and subseafloor cell concentrations, and fitting to observed hydrogen and methane concentrations in the venting fluid, the subseafloor biomass, fluid residence time, and methane production rate can be constrained.

Cold Osmotic Shock in Saccharomyces cerevisiae

PubMed Central

Patching, J. W.; Rose, A. H.

1971-01-01

Saccharomyces cerevisiae NCYC 366 is susceptible to cold osmotic shock. Exponentially growing cells from batch cultures grown in defined medium at 30 C, after being suspended in 0.8 m mannitol containing 10 mm ethylenedia-minetetraacetic acid and then resuspended in ice-cold 0.5 mm MgCl2, accumulated the nonmetabolizable solutes d-glucosamine-hydrochloride and 2-aminoisobutyrate at slower rates than unshocked cells; shocked cells retained their viability. Storage of unshocked batch-grown cells in buffer at 10 C led to an increase in ability to accumulate glucosamine, and further experiments were confined to cells grown in a chemostat under conditions of glucose limitation, thereby obviating the need for storing cells before use. A study was made of the effect of the different stages in the cold osmotic shock procedure, including the osmotic stress, the chelating agent, and the cold Mg2+-containing diluent, on viability and solute-accumulating ability. Growth of shocked cells in defined medium resembled that of unshocked cells; however, in malt extract-yeast extract-glucose-peptone medium, the shocked cells had a longer lag phase of growth and initially grew at a slower rate. Cold osmotic shock caused the release of low-molecular-weight compounds and about 6 to 8% of the cell protein. Neither the cell envelope enzymes, invertase, acid phosphatase and l-leucine-β-naphthylamidase, nor the cytoplasmic enzyme, alkaline phosphatase, were released when yeast cells were subjected to cold osmotic shock. PMID:5001201

Influence of methanol/sorbitol co-feeding rate on pAOX1 induction in a Pichia pastoris Mut+ strain in bioreactor with limited oxygen transfer rate.

PubMed

Carly, F; Niu, H; Delvigne, F; Fickers, P

2016-04-01

High Pichia pastoris biomass density could be obtained using high co-feeding rate of methanol and sorbitol in a fed-batch or continuous culture, while further higher feeding rate finally leads to oxygen limitation in bioreactor. In the literature, there is lack of report about AOX1 promoter regulation with regard to dissolved oxygen level (DO). Therefore, in this work, chemostat cultures were performed to investigate the cell growth, metabolism and regulation of the AOX1 promoter (pAOX1) regarding co-feeding rate of optimized methanol/sorbitol mixture (methanol fraction 0.60 C-mol/C-mol) using a P. pastoris Mut+/pAOX1-lacZ strain. The oxygen transfer rates (OTR) in bioreactor were kept in the range of typical values of large bioreactor, i.e., 4-8 g/(L h) if DO equals 30 % saturation or 5-10 g/(L h) if DO nears zero. For DO >0, an increase of the carbon fed led to an increase of pAOX1 induction. By contrast, when dissolved oxygen was completely depleted, methanol accumulated, causing a 30 % decrease of pAOX1 induction. However, this decrease is more likely to be lined to methanol accumulation than to low level of dissolved oxygen (<4 % DO). Methanol/sorbitol co-feeding allowed cells to adapt to oxygen transient limitations that often occur at industrial scale with reduced effect on pAOX1 induction. The optimal feeding rate tested here was 6.6 mmol C (DCW h)(-1) at an OTR of 8.28 g O2(L h)(-1) with over fivefold pAOX1 induction (probably directly associated with target protein productivity) compared with previous work.

Metastable coexistence of multiple genotypes in a constant environment with a single resource through fixed settings of a multiplication-survival trade-off.

PubMed

Maharjan, Ram; Ferenci, Thomas

2016-04-01

The biological complexity of trade-offs has been a major obstacle in understanding bacterial diversity and coexistence. Here we reduce the biological complexity by using isogenic Escherichia coli strains differing only in a multiplication-survival trade-off regulated by RpoS. The contribution of trade-off characteristics to fitness in different environments was determined. We then designed an environment with intermediate-stress levels that elicits an equivalent fitness. We found metastable coexistence of three strains in steady-state chemostats until mutations changed the relative fitness of competing strains. Our results help explain the rich intra- and inter-species diversity of bacteria through alternative settings of relatively few trade-offs. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Modeling of scale-dependent bacterial growth by chemical kinetics approach.

PubMed

Martínez, Haydee; Sánchez, Joaquín; Cruz, José-Manuel; Ayala, Guadalupe; Rivera, Marco; Buhse, Thomas

2014-01-01

We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V) of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

PubMed Central

Lezon, Timothy R.; Banavar, Jayanth R.; Cieplak, Marek; Maritan, Amos; Fedoroff, Nina V.

2006-01-01

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems. PMID:17138668

[Biomass composition of thermotolerant yeasts of the genus Candida under elevated cultivation temperatures].

PubMed

Chistiakova, T I; Dediukhina, E G; Eroshin, V K

1981-01-01

The effect of growth temperature on the content of nucleic acids, the content and composition of protein, and the pool of free amino acids and lipids was studied under the conditions of chemostat cultivation of yeast strains at constant flow rates and pO2. The pool of free amino acids in all of the strains decreased with an increase in the temperature of growth. Changes in the content and composition of other cellular components depending on temperature were determined by individual characteristics of the strains. A linear relationship between the content of biomass components and the temperature of growth was found only in Candida scottii. The temperature of yeast cultivation may be used as a factor regulating the pool of free intracellular amino acids and the fatty acids composition of lipids.

Application of a microcomputer-based system to control and monitor bacterial growth.

PubMed

Titus, J A; Luli, G W; Dekleva, M L; Strohl, W R

1984-02-01

A modular microcomputer-based system was developed to control and monitor various modes of bacterial growth. The control system was composed of an Apple II Plus microcomputer with 64-kilobyte random-access memory; a Cyborg ISAAC model 91A multichannel analog-to-digital and digital-to-analog converter; paired MRR-1 pH, pO(2), and foam control units; and in-house-designed relay, servo control, and turbidimetry systems. To demonstrate the flexibility of the system, we grew bacteria under various computer-controlled and monitored modes of growth, including batch, turbidostat, and chemostat systems. The Apple-ISAAC system was programmed in Labsoft BASIC (extended Applesoft) with an average control program using ca. 6 to 8 kilobytes of memory and up to 30 kilobytes for datum arrays. This modular microcomputer-based control system was easily coupled to laboratory scale fermentors for a variety of fermentations.

Application of a Microcomputer-Based System to Control and Monitor Bacterial Growth

PubMed Central

Titus, Jeffrey A.; Luli, Gregory W.; Dekleva, Michael L.; Strohl, William R.

1984-01-01

A modular microcomputer-based system was developed to control and monitor various modes of bacterial growth. The control system was composed of an Apple II Plus microcomputer with 64-kilobyte random-access memory; a Cyborg ISAAC model 91A multichannel analog-to-digital and digital-to-analog converter; paired MRR-1 pH, pO2, and foam control units; and in-house-designed relay, servo control, and turbidimetry systems. To demonstrate the flexibility of the system, we grew bacteria under various computer-controlled and monitored modes of growth, including batch, turbidostat, and chemostat systems. The Apple-ISAAC system was programmed in Labsoft BASIC (extended Applesoft) with an average control program using ca. 6 to 8 kilobytes of memory and up to 30 kilobytes for datum arrays. This modular microcomputer-based control system was easily coupled to laboratory scale fermentors for a variety of fermentations. PMID:16346462

A size-structured model of bacterial growth and reproduction.

PubMed

Ellermeyer, S F; Pilyugin, S S

2012-01-01

We consider a size-structured bacterial population model in which the rate of cell growth is both size- and time-dependent and the average per capita reproduction rate is specified as a model parameter. It is shown that the model admits classical solutions. The population-level and distribution-level behaviours of these solutions are then determined in terms of the model parameters. The distribution-level behaviour is found to be different from that found in similar models of bacterial population dynamics. Rather than convergence to a stable size distribution, we find that size distributions repeat in cycles. This phenomenon is observed in similar models only under special assumptions on the functional form of the size-dependent growth rate factor. Our main results are illustrated with examples, and we also provide an introductory study of the bacterial growth in a chemostat within the framework of our model.

Competition for nutrients and light: testing advances in resource competition with a natural phytoplankton community.

PubMed

Burson, Amanda; Stomp, Maayke; Greenwell, Emma; Grosse, Julia; Huisman, Jef

2018-05-01

A key challenge in ecology is to understand how nutrients and light affect the biodiversity and community structure of phytoplankton and plant communities. According to resource competition models, ratios of limiting nutrients are major determinants of species composition. At high nutrient levels, however, species interactions may shift to competition for light, which might make nutrient ratios less relevant. The "nutrient-load hypothesis" merges these two perspectives, by extending the classic model of competition for two nutrients to include competition for light. Here, we test five key predictions of the nutrient-load hypothesis using multispecies competition experiments. A marine phytoplankton community sampled from the North Sea was inoculated in laboratory chemostats provided with different nitrogen (N) and phosphorus (P) loads to induce either single resource limitation or co-limitation of N, P, and light. Four of the five predictions were validated by the experiments. In particular, different resource limitations favored the dominance of different species. Increasing nutrient loads caused changes in phytoplankton species composition, even if the N:P ratio of the nutrient loads remained constant, by shifting the species interactions from competition for nutrients to competition for light. In all treatments, small species became dominant whereas larger species were competitively excluded, supporting the common view that small cell size provides a competitive advantage under resource-limited conditions. Contrary to expectation, all treatments led to coexistence of diatoms, cyanobacteria and green algae, resulting in a higher diversity of species than predicted by theory. Because the coexisting species comprised three phyla with different photosynthetic pigments, we speculate that niche differentiation in the light spectrum might play a role. Our results show that mechanistic resource competition models that integrate nutrient-based and light-based approaches provide an important step forward to understand and predict how changing nutrient loads affect community composition. © 2018 The Authors Ecology published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.

Rising CO2 Levels Will Intensify Phytoplankton Blooms in Eutrophic and Hypertrophic Lakes

PubMed Central

Verspagen, Jolanda M. H.; Van de Waal, Dedmer B.; Finke, Jan F.; Visser, Petra M.; Van Donk, Ellen; Huisman, Jef

2014-01-01

Harmful algal blooms threaten the water quality of many eutrophic and hypertrophic lakes and cause severe ecological and economic damage worldwide. Dense blooms often deplete the dissolved CO2 concentration and raise pH. Yet, quantitative prediction of the feedbacks between phytoplankton growth, CO2 drawdown and the inorganic carbon chemistry of aquatic ecosystems has received surprisingly little attention. Here, we develop a mathematical model to predict dynamic changes in dissolved inorganic carbon (DIC), pH and alkalinity during phytoplankton bloom development. We tested the model in chemostat experiments with the freshwater cyanobacterium Microcystis aeruginosa at different CO2 levels. The experiments showed that dense blooms sequestered large amounts of atmospheric CO2, not only by their own biomass production but also by inducing a high pH and alkalinity that enhanced the capacity for DIC storage in the system. We used the model to explore how phytoplankton blooms of eutrophic waters will respond to rising CO2 levels. The model predicts that (1) dense phytoplankton blooms in low- and moderately alkaline waters can deplete the dissolved CO2 concentration to limiting levels and raise the pH over a relatively wide range of atmospheric CO2 conditions, (2) rising atmospheric CO2 levels will enhance phytoplankton blooms in low- and moderately alkaline waters with high nutrient loads, and (3) above some threshold, rising atmospheric CO2 will alleviate phytoplankton blooms from carbon limitation, resulting in less intense CO2 depletion and a lesser increase in pH. Sensitivity analysis indicated that the model predictions were qualitatively robust. Quantitatively, the predictions were sensitive to variation in lake depth, DIC input and CO2 gas transfer across the air-water interface, but relatively robust to variation in the carbon uptake mechanisms of phytoplankton. In total, these findings warn that rising CO2 levels may result in a marked intensification of phytoplankton blooms in eutrophic and hypertrophic waters. PMID:25119996

Oxygen- and NssR-dependent Globin Expression and Enhanced Iron Acquisition in the Response of Campylobacter to Nitrosative Stress*S⃞

PubMed Central

Monk, Claire E.; Pearson, Bruce M.; Mulholland, Francis; Smith, Holly K.; Poole, Robert K.

2008-01-01

Pathogenic bacteria experience nitrosative stress from NO generated in the host and from nitrosating species such as S-nitrosoglutathione. The food-borne pathogen Campylobacter jejuni responds by activating gene expression from a small regulon under the control of the NO-sensitive regulator, NssR. Here, we describe the full extent of the S-nitrosoglutathione response using transcriptomic and proteomic analysis of batch- and chemostat-cultured C. jejuni. In addition to the NssR regulon, which includes two hemoglobins (Cgb and Ctb), we identify more than 90 other up-regulated genes, notably those encoding heat shock proteins and proteins involved in oxidative stress tolerance and iron metabolism/transport. Up-regulation of a subset of these genes, including cgb, is also elicited by NO-releasing compounds. Mutation of the iron-responsive regulator Fur results in insensitivity of growth to NO, suggesting that derepression of iron-regulated genes and augmentation of iron acquisition is a physiological response to nitrosative damage. We describe the effect of oxygen availability on nitrosative stress tolerance; cells cultured at higher rates of oxygen diffusion have elevated levels of hemoglobins, are more resistant to inhibition by NO of both growth and respiration, and consume NO more rapidly. The oxygen response is mediated by NssR. Thus, in addition to NO detoxification catalyzed by the hemoglobins Cgb and possibly Ctb, C. jejuni mounts an extensive stress response. We suggest that inhibition of respiration by NO may increase availability of oxygen for Cgb synthesis and function. PMID:18682395

A multiplex culture system for the long‐term growth of fission yeast cells

PubMed Central

Callens, Céline; Coelho, Nelson C.; Miller, Aaron W.; Sananes, Maria Rosa Domingo; Dunham, Maitreya J.; Denoual, Matthieu

2017-01-01

Abstract Maintenance of long‐term cultures of yeast cells is central to a broad range of investigations, from metabolic studies to laboratory evolution assays. However, repeated dilutions of batch cultures lead to variations in medium composition, with implications for cell physiology. In Saccharomyces cerevisiae, powerful miniaturized chemostat setups, or ministat arrays, have been shown to allow for constant dilution of multiple independent cultures. Here we set out to adapt these arrays for continuous culture of a morphologically and physiologically distinct yeast, the fission yeast Schizosaccharomyces pombe, with the goal of maintaining constant population density over time. First, we demonstrated that the original ministats are incompatible with growing fission yeast for more than a few generations, prompting us to modify different aspects of the system design. Next, we identified critical parameters for sustaining unbiased vegetative growth in these conditions. This requires deletion of the gsf2 flocculin‐encoding gene, along with addition of galactose to the medium and lowering of the culture temperature. Importantly, we improved the flexibility of the ministats by developing a piezo‐pump module for the independent regulation of the dilution rate of each culture. This made it possible to easily grow strains that have different generation times in the same assay. Our system therefore allows for maintaining multiple fission yeast cultures in exponential growth, adapting the dilution of each culture over time to keep constant population density for hundreds of generations. These multiplex culture systems open the door to a new range of long‐term experiments using this model organism. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd. PMID:28426144

The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae.

PubMed

Bracher, Jasmine M; Verhoeven, Maarten D; Wisselink, H Wouter; Crimi, Barbara; Nijland, Jeroen G; Driessen, Arnold J M; Klaassen, Paul; van Maris, Antonius J A; Daran, Jean-Marc G; Pronk, Jack T

2018-01-01

l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains. Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures. Of five genes, that encoded putative transport proteins and showed an over 30-fold higher transcript level in l-arabinose-grown cultures compared to d-glucose-grown cultures, only one (Pc20g01790) restored growth on l-arabinose upon expression in an engineered l-arabinose-fermenting S. cerevisiae strain in which the endogenous l-arabinose transporter, GAL2 , had been deleted. Sugar transport assays indicated that this fungal transporter, designated as Pc AraT, is a high-affinity ( K m  = 0.13 mM), high-specificity l-arabinose-proton symporter that does not transport d-xylose or d-glucose. An l-arabinose-metabolizing S. cerevisiae strain in which GAL2 was replaced by PcaraT showed 450-fold lower residual substrate concentrations in l-arabinose-limited chemostat cultures than a congenic strain in which l-arabinose import depended on Gal2 (4.2 × 10 -3 and 1.8 g L -1 , respectively). Inhibition of l-arabinose transport by the most abundant sugars in hydrolysates, d-glucose and d-xylose was far less pronounced than observed with Gal2. Expression of Pc AraT in a hexose-phosphorylation-deficient, l-arabinose-metabolizing S. cerevisiae strain enabled growth in media supplemented with both 20 g L -1 l-arabinose and 20 g L -1 d-glucose, which completely inhibited growth of a congenic strain in the same condition that depended on l-arabinose transport via Gal2. Its high affinity and specificity for l-arabinose, combined with limited sensitivity to inhibition by d-glucose and d-xylose, make Pc AraT a valuable transporter for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.

Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.

PubMed

Chumnanpuen, Pramote; Nookaew, Intawat; Nielsen, Jens

2013-10-16

In the yeast Saccharomyces cerevisiae, genes containing UASINO sequences are regulated by the Ino2/Ino4 and Opi1 transcription factors, and this regulation controls lipid biosynthesis. The expression level of INO2 and INO4 genes (INO-level) at different nutrient limited conditions might lead to various responses in yeast lipid metabolism. In this study, we undertook a global study on how INO-levels (transcription level of INO2 and INO4) affect lipid metabolism in yeast and we also studied the effects of single and double deletions of the two INO-genes (deficient effect). Using 2 types of nutrient limitations (carbon and nitrogen) in chemostat cultures operated at a fixed specific growth rate of 0.1 h-1 and strains having different INO-level, we were able to see the effect on expression level of the genes involved in lipid biosynthesis and the fluxes towards the different lipid components. Through combined measurements of the transcriptome, metabolome, and lipidome it was possible to obtain a large dataset that could be used to identify how the INO-level controls lipid metabolism and also establish correlations between the different components. In this study, we undertook a global study on how INO-levels (transcription level of INO2 and INO4) affect lipid metabolism in yeast and we also studied the effects of single and double deletions of the two INO-genes (deficient effect). Using 2 types of nutrient limitations (carbon and nitrogen) in chemostat cultures operated at a fixed specific growth rate of 0.1 h-1 and strains having different INO-level, we were able to see the effect on expression level of the genes involved in lipid biosynthesis and the fluxes towards the different lipid components. Through combined measurements of the transcriptome, metabolome, and lipidome it was possible to obtain a large dataset that could be used to identify how the INO-level controls lipid metabolism and also establish correlations between the different components. Our analysis showed the strength of using a combination of transcriptome and lipidome analysis to illustrate the effect of INO-levels on phospholipid metabolism and based on our analysis we established a global regulatory map.

Pichia pastoris Exhibits High Viability and a Low Maintenance Energy Requirement at Near-Zero Specific Growth Rates

PubMed Central

Rebnegger, Corinna; Vos, Tim; Graf, Alexandra B.; Valli, Minoska; Pronk, Jack T.

2016-01-01

ABSTRACT The yeast Pichia pastoris is a widely used host for recombinant protein production. Understanding its physiology at extremely low growth rates is a first step in the direction of decoupling product formation from cellular growth and therefore of biotechnological relevance. Retentostat cultivation is an excellent tool for studying microbes at extremely low specific growth rates but has so far not been implemented for P. pastoris. Retentostat feeding regimes were based on the maintenance energy requirement (mS) and maximum biomass yield on glucose (YX/Smax) estimated from steady-state glucose-limited chemostat cultures. Aerobic retentostat cultivation enabled reproducible, smooth transitions from a specific growth rate (μ) of 0.025 h−1 to near-zero specific growth rates (μ < 0.001 h−1). At these near-zero specific growth rates, viability remained at least 97%. The value of mS at near-zero growth rates was 3.1 ± 0.1 mg glucose per g biomass and h, which was 3-fold lower than the mS estimated from faster-growing chemostat cultures. This difference indicated that P. pastoris reduces its maintenance energy requirement at extremely low μ, a phenomenon not previously observed in eukaryotes. Intracellular levels of glycogen and trehalose increased, while μ progressively declined during retentostat cultivation. Transcriptional reprogramming toward zero growth included the upregulation of many transcription factors as well as stress-related genes and the downregulation of cell cycle genes. This study underlines the relevance of comparative analysis of maintenance energy metabolism, which has an important impact on large-scale industrial processes. IMPORTANCE The yeast Pichia pastoris naturally lives on trees and can utilize different carbon sources, among them glucose, glycerol, and methanol. In biotechnology, it is widely used for the production of recombinant proteins. For both the understanding of life in its natural habitat and optimized production processes, a better understanding of cell physiology at an extremely low growth rate would be of extraordinary value. Therefore, we have grown P. pastoris in a retentostat, which allows the cultivation of metabolically active cells even at zero growth. Here we reached doubling times as long as 38 days and found that P. pastoris decreases its maintenance energy demand 3-fold during very slow growth, which enables it to survive with a much lower substrate supply than baker's yeast. PMID:27208115

Use of carbon steel ball bearings to determine the effect of biocides and corrosion inhibitors on microbiologically influenced corrosion under flow conditions.

PubMed

Pinnock, Tijan; Voordouw, Johanna; Voordouw, Gerrit

2018-05-10

A consortium of sulfate-reducing bacteria consisting mostly of Desulfovibrio, Desulfomicrobium, and Desulfocurvus from oil field produced water was cultivated in a chemostat, receiving medium with 20 mM formate and 10 mM sulfate as the energy and 1 mM acetate as the carbon source. The chemostat effluent, containing 5 mM sulfide and 0.5 mM of residual acetate, was passed through 1-ml syringe columns with 60 carbon steel ball bearings (BBs) of 53.6 ± 0.1 mg each at a flow rate of 0.8 ml/h per column. These were treated every 5 days with 1.6 ml of 300 ppm of glutaraldehyde (Glut), tetrakis(hydroxymethyl)phosphonium sulfate (THPS), benzalkonium chloride (BAC), or Glut/BAC, a mixture of Glut and BAC. Alternatively, BBs were treated with 33% (v/v) of a water-soluble (CR_W) or an oil-soluble (CR_O1 or CR_O3) corrosion inhibitor for 20 s after which the corrosion inhibitor was drained off and BBs were packed into columns. The effluent of untreated control columns had no acetate. Treatment with the chemically reactive biocides Glut and THPS, as well as with Glut/BAC, gave a transient increase of acetate indicating decreased microbial activity. This was not seen with BAC alone indicating it to be the least effective biocide. Relative to untreated BBs (100%), those treated periodically with Glut, THPS, BAC, or Glut/BAC had a general weight loss corrosion rate of 91, 81, 45, and 36% of the untreated rate of 0.104 ± 0.004 mm/year, respectively. Single treatment with corrosion inhibitors decreased corrosion to 48, 2, and 1% of the untreated rate for CR_W, CR_O1 and CR_O3, respectively. Analysis of the distribution of corrosion rates from the weight loss of individual BBs (N = 120) indicated the presence of a more slowly and a more rapidly corroding group. BAC treatment prevented emergence of the latter, and this quaternary ammonium detergent appeared most effective in decreasing corrosion not because of its biocidal properties, but because of its corrosion inhibitory properties.

Effects of Bacterial Host and Dichloromethane Dehalogenase on the Competitiveness of Methylotrophic Bacteria Growing with Dichloromethane

PubMed Central

Gisi, Daniel; Willi, Laurent; Traber, Hubert; Leisinger, Thomas; Vuilleumier, Stéphane

1998-01-01

Methylobacterium sp. strain DM4 and Methylophilus sp. strain DM11 can grow with dichloromethane (DCM) as the sole source of carbon and energy by virtue of homologous glutathione-dependent DCM dehalogenases with markedly different kinetic properties (the kcat values of the enzymes of these strains are 0.6 and 3.3 s−1, respectively, and the Km values are 9 and 59 μM, respectively). These strains, as well as transconjugant bacteria expressing the DCM dehalogenase gene (dcmA) from DM11 or DM4 on a broad-host-range plasmid in the background of dcmA mutant DM4-2cr, were investigated by growing them under growth-limiting conditions and in the presence of an excess of DCM. The maximal growth rates and maximal levels of dehalogenase for chemostat-adapted bacteria were higher than the maximal growth rates and maximal levels of dehalogenase for batch-grown bacteria. The substrate saturation constant of strain DM4 was much lower than the Km of its associated dehalogenase, suggesting that this strain is adapted to scavenge low concentrations of DCM. Strains and transconjugants expressing the DCM dehalogenase from strain DM11, on the other hand, had higher growth rates than bacteria expressing the homologous dehalogenase from strain DM4. Competition experiments performed with pairs of DCM-degrading strains revealed that a strain expressing the dehalogenase from DM4 had a selective advantage in continuous culture under substrate-limiting conditions, while strains expressing the DM11 dehalogenase were superior in batch culture when there was an excess of substrate. Only DCM-degrading bacteria with a dcmA gene similar to that from strain DM4, however, were obtained in batch enrichment cultures prepared with activated sludge from sewage treatment plants. PMID:9546153

A multiplex culture system for the long-term growth of fission yeast cells.

PubMed

Callens, Céline; Coelho, Nelson C; Miller, Aaron W; Sananes, Maria Rosa Domingo; Dunham, Maitreya J; Denoual, Matthieu; Coudreuse, Damien

2017-08-01

Maintenance of long-term cultures of yeast cells is central to a broad range of investigations, from metabolic studies to laboratory evolution assays. However, repeated dilutions of batch cultures lead to variations in medium composition, with implications for cell physiology. In Saccharomyces cerevisiae, powerful miniaturized chemostat setups, or ministat arrays, have been shown to allow for constant dilution of multiple independent cultures. Here we set out to adapt these arrays for continuous culture of a morphologically and physiologically distinct yeast, the fission yeast Schizosaccharomyces pombe, with the goal of maintaining constant population density over time. First, we demonstrated that the original ministats are incompatible with growing fission yeast for more than a few generations, prompting us to modify different aspects of the system design. Next, we identified critical parameters for sustaining unbiased vegetative growth in these conditions. This requires deletion of the gsf2 flocculin-encoding gene, along with addition of galactose to the medium and lowering of the culture temperature. Importantly, we improved the flexibility of the ministats by developing a piezo-pump module for the independent regulation of the dilution rate of each culture. This made it possible to easily grow strains that have different generation times in the same assay. Our system therefore allows for maintaining multiple fission yeast cultures in exponential growth, adapting the dilution of each culture over time to keep constant population density for hundreds of generations. These multiplex culture systems open the door to a new range of long-term experiments using this model organism. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd.

Thermodynamic controls on the kinetics of microbial low-pH Fe(II) oxidation.

PubMed

Larson, Lance N; Sánchez-España, Javier; Kaley, Bradley; Sheng, Yizhi; Bibby, Kyle; Burgos, William D

2014-08-19

Acid mine drainage (AMD) is a major worldwide environmental threat to surface and groundwater quality. Microbial low-pH Fe(II) oxidation could be exploited for cost-effective AMD treatment; however, its use is limited because of uncertainties associated with its rate and ability to remove Fe from solution. We developed a thermodynamic-based framework to evaluate the kinetics of low-pH Fe(II) oxidation. We measured the kinetics of low-pH Fe(II) oxidation at five sites in the Appalachian Coal Basin in the US and three sites in the Iberian Pyrite Belt in Spain and found that the fastest rates of Fe(II) oxidation occurred at the sites with the lowest pH values. Thermodynamic calculations showed that the Gibbs free energy of Fe(II) oxidation (ΔG(oxidation)) was also most negative at the sites with the lowest pH values. We then conducted two series of microbial Fe(II) oxidation experiments in laboratory-scale chemostatic bioreactors operated through a series of pH values (2.1-4.2) and found the same relationships between Fe(II) oxidation kinetics, ΔG(oxidation), and pH. Conditions that favored the fastest rates of Fe(II) oxidation coincided with higher Fe(III) solubility. The solubility of Fe(III) minerals, thus plays an important role on Fe(II) oxidation kinetics. Methods to incorporate microbial low-pH Fe(II) oxidation into active and passive AMD treatment systems are discussed in the context of these findings. This study presents a simplified model that describes the relationship between free energy and microbial kinetics and should be broadly applicable to many biogeochemical systems.

Impacts of chemical gradients on microbial community structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Effects of Limited Aeration and of the ArcAB System on Intermediary Pyruvate Catabolism in Escherichia coli

PubMed Central

Alexeeva, Svetlana; de Kort, Bart; Sawers, Gary; Hellingwerf, Klaas J.; de Mattos, M. Joost Teixeira

2000-01-01

The capacity of Escherichia coli to adapt its catabolism to prevailing redox conditions resides mainly in three catabolic branch points involving (i) pyruvate formate-lyase (PFL) and the pyruvate dehydrogenase complex (PDHc), (ii) the exclusively fermentative enzymes and those of the Krebs cycle, and (iii) the alternative terminal cytochrome bd and cytochrome bo oxidases. A quantitative analysis of the relative catabolic fluxes through these pathways is presented for steady-state glucose-limited chemostat cultures with controlled oxygen availability ranging from full aerobiosis to complete anaerobiosis. Remarkably, PFL contributed significantly to the catabolic flux under microaerobic conditions and was found to be active simultaneously with PDHc and cytochrome bd oxidase-dependent respiration. The synthesis of PFL and cytochrome bd oxidase was found to be maximal in the lower microaerobic range but not in a ΔArcA mutant, and we conclude that the Arc system is more active with respect to regulation of these two positively regulated operons during microaerobiosis than during anaerobiosis. PMID:10940038

Anaerobic biodegradation of soybean biodiesel and diesel blends under methanogenic conditions.

PubMed

Wu, Shuyun; Yassine, Mohamad H; Suidan, Makram T; Venosa, Albert D

2015-12-15

Biotransformation of soybean biodiesel and the inhibitory effect of petrodiesel were studied under methanogenic conditions. Biodiesel removal efficiency of more than 95% was achieved in a chemostat with influent biodiesel concentrations up to 2.45 g/L. The kinetics of anaerobic biodegradation of soybean biodiesel B100 (biodiesel only) with different petrodiesel loads was studied using biomass pre-acclimated to B100 and B80 (80% biodiesel and 20% petrodiesel). The results indicated that the biodiesel fraction of the blend could be effectively biodegraded, whereas petrodiesel was not biodegraded at all under methanogenic conditions. The presence of petrodiesel in blends with biodiesel had a greater inhibitory effect on the rate of biodegradation than the biodegradation efficiency (defined as the efficiency of methane production). Both the biodegradation rate coefficient and the methane production efficiency increased almost linearly with the increasing fraction of biodiesel. With the increasing fraction of petrodiesel, the biodegradation rate and efficiency were correlated with the concentration of soluble FAMEs in the water. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impacts of chemical gradients on microbial community structure

DOE PAGES

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.; ...

2017-01-17

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Brady D.; Apel, William A.; DeVeaux, Linda C.

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. A. acidocaldarius grew while simultaneouslymore » metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two. Regulation occurred primarily in genes: 1) encoding regulators, 2) encoding enzymes for cell synthesis, and 3) encoding sugar transporters.« less

Impacts of chemical gradients on microbial community structure

PubMed Central

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-01-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems. PMID:28094795

Impacts of chemical gradients on microbial community structure.

PubMed

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-04-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

An incoherent feedforward loop facilitates adaptive tuning of gene expression.

PubMed

Hong, Jungeui; Brandt, Nathan; Abdul-Rahman, Farah; Yang, Ally; Hughes, Tim; Gresham, David

2018-04-05

We studied adaptive evolution of gene expression using long-term experimental evolution of Saccharomyces cerevisiae in ammonium-limited chemostats. We found repeated selection for non-synonymous variation in the DNA binding domain of the transcriptional activator, GAT1, which functions with the repressor, DAL80 in an incoherent type-1 feedforward loop (I1-FFL) to control expression of the high affinity ammonium transporter gene, MEP2. Missense mutations in the DNA binding domain of GAT1 reduce its binding to the GATAA consensus sequence. However, we show experimentally, and using mathematical modeling, that decreases in GAT1 binding result in increased expression of MEP2 as a consequence of properties of I1-FFLs. Our results show that I1-FFLs, one of the most commonly occurring network motifs in transcriptional networks, can facilitate adaptive tuning of gene expression through modulation of transcription factor binding affinities. Our findings highlight the importance of gene regulatory architectures in the evolution of gene expression. © 2018, Hong et al.

Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools

PubMed Central

Reznik, Ed; Mehta, Pankaj; Segrè, Daniel

2013-01-01

Stoichiometric models of metabolism, such as flux balance analysis (FBA), are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances) are informative of some features of in vivo metabolite concentrations. Mathematically, the sensitivity of FBA to these flux imbalances is captured by a native feature of linear optimization, the dual problem, and its corresponding variables, known as shadow prices. First, using recently published data on chemostat growth of Saccharomyces cerevisae under different nutrient limitations, we show that shadow prices anticorrelate with experimentally measured degrees of growth limitation of intracellular metabolites. We next hypothesize that metabolites which are limiting for growth (and thus have very negative shadow price) cannot vary dramatically in an uncontrolled way, and must respond rapidly to perturbations. Using a collection of published datasets monitoring the time-dependent metabolomic response of Escherichia coli to carbon and nitrogen perturbations, we test this hypothesis and find that metabolites with negative shadow price indeed show lower temporal variation following a perturbation than metabolites with zero shadow price. Finally, we illustrate the broader applicability of flux imbalance analysis to other constraint-based methods. In particular, we explore the biological significance of shadow prices in a constraint-based method for integrating gene expression data with a stoichiometric model. In this case, shadow prices point to metabolites that should rise or drop in concentration in order to increase consistency between flux predictions and gene expression data. In general, these results suggest that the sensitivity of metabolic optima to violations of the steady state constraints carries biologically significant information on the processes that control intracellular metabolites in the cell. PMID:24009492

Gained insights from combined high-frequency and long-term water quality monitoring in agricultural catchments

NASA Astrophysics Data System (ADS)

Jomaa, Seifeddine; Dupas, Rémi; Musolff, Andreas; Rozemeijer, Joachim; Borchardt, Dietrich; Rode, Michael

2017-04-01

Despite extensive efforts to reduce nitrate (NO3) transfer in agricultural areas, the NO3 concentration in rivers often changes little. To investigate the reasons for this limited response, NO3 dynamics in a 100 km2 agricultural catchment in eastern Germany was analysed from decadal to infra-hourly time scales. First, Dynamic Harmonic Regression (DHR) analysis of a 32-year (1982-2014) record of NO3 and discharge revealed that i) the long-term trend in NO3 concentration was closely related to that in discharge, suggesting that large-scale weather and climate patterns were masking the effect of improved nitrogen management on NO3 trends; ii) maximum winter and minimum summer concentrations had a persistent seasonal pattern, which was interpreted as a dynamic NO3 concentration from the soil and subsoil columns; and iii) the catchment progressively changed from chemodynamic to more chemostatic behaviour over the three decades of study, which is a sign of long-term homogenisation of NO3 concentrations in the profile. Second, infra-hourly (15 min time interval) analysis of storm-event dynamics during a typical hydrological year (2005-2006) was performed to identify periods of the year with high leaching risk and to link the latter to agricultural management practices in the catchment. Also, intra-hourly data was used to improve NO3 load estimation during storm events. An Event Response Reconstruction (ERR) model was built using NO3 concentration response descriptor variables and predictor variables deduced from discharge and precipitation records. The ERR approach significantly improved NO3 load estimates compared to linear interpolation of grab-sampling data (error was reduced from 10 to 1%). Finally, this study shows that detailed physical understanding of NO3 dynamics across time scales can be obtained only through combined analysis of long-term records and high-resolution sensor data. Hence, a joint effort is advocated between environmental authorities, who usually perform long-term monitoring, and scientific programmes, which usually perform high-resolution monitoring.

Short- and Long-Term Effects of Cumulative Finals on Student Learning

ERIC Educational Resources Information Center

Khanna, Maya M.; Brack, Amy S. Badura; Finken, Laura L.

2013-01-01

In two experiments, we examined the benefits of cumulative and noncumulative finals on students' short- and long-term course material retention. In Experiment 1, we examined results from course content exams administered immediately after course finals. Course sections including cumulative finals had higher content exam scores than sections…

International electives in the final year of German medical school education--a student's perspective.

PubMed

Ebrahimi-Fakhari, Darius; Agrawal, Mridul; Wahlster, Lara

2014-01-01

The final year of medical school has a unique role for introducing students to their future responsibilities and challenges. At many medical schools, electives at an accredited institution abroad are a common part of the student's final year experience. International electives provide an opportunity for a personal and academic experience that will often create new perspectives on clinical medicine and research, medical education and healthcare policy. In this article the authors reflect on their experience as elective students abroad and discuss the contribution of international electives to the constant development and progress of local final year rotations. They identify key areas for improving final year electives and outline essential features for a valuable and successful final year elective.

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.

PubMed

Card, Roderick M; Cawthraw, Shaun A; Nunez-Garcia, Javier; Ellis, Richard J; Kay, Gemma; Pallen, Mark J; Woodward, Martin J; Anjum, Muna F

2017-07-18

The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase bla CTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies. IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies. Copyright © 2017 Card et al.

Sulfur Isotope Effects of Dissimilatory Sulfite Reductase

PubMed Central

Leavitt, William D.; Bradley, Alexander S.; Santos, André A.; Pereira, Inês A. C.; Johnston, David T.

2015-01-01

The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/32S, 36S/32S) sulfur isotope fractionations imparted by a central enzyme in the energy metabolism of sulfate reducers, dissimilatory sulfite reductase (DsrAB). Results from in vitro sulfite reduction experiments allow us to calculate the in vitro DsrAB isotope effect in 34S/32S (hereafter, 34εDsrAB) to be 15.3 ± 2‰, 2σ. The accompanying minor isotope effect in 33S, described as 33λDsrAB, is calculated to be 0.5150 ± 0.0012, 2σ. These observations facilitate a rigorous evaluation of the isotopic fractionation associated with the dissimilatory MSR pathway, as well as of the environmental variables that govern the overall magnitude of fractionation by natural communities of sulfate reducers. The isotope effect induced by DsrAB upon sulfite reduction is a factor of 0.3–0.6 times prior indirect estimates, which have ranged from 25 to 53‰ in 34εDsrAB. The minor isotope fractionation observed from DsrAB is consistent with a kinetic or equilibrium effect. Our in vitro constraints on the magnitude of 34εDsrAB is similar to the median value of experimental observations compiled from all known published work, where 34εr−p = 16.1‰ (r–p indicates reactant vs. product, n = 648). This value closely matches those of MSR operating at high sulfate reduction rates in both laboratory chemostat experiments (34εSO4−H2S =  17.3 ± 1.5‰, 2σ) and in modern marine sediments (34εSO4−H2S =  17.3 ± 3.8‰). Targeting the direct isotopic consequences of a specific enzymatic processes is a fundamental step toward a biochemical foundation for reinterpreting the biogeochemical and geobiological sulfur isotope records in modern and ancient environments. PMID:26733949

Reactions of Thiocyanate Ions with Acid: A Laboratory Experiment.

ERIC Educational Resources Information Center

Glidewell, Christopher; And Others

1984-01-01

Background information, procedures, and typical results are provided for a three-part experiment involving reactions of potassium thiocynate (KNCS) with sulfuric acid. The experiment represents the final stage of structured work prior to students' research projects during their final year. (JM)

Retrieval enhances eyewitness suggestibility to misinformation in free and cued recall.

PubMed

Wilford, Miko M; Chan, Jason C K; Tuhn, Sam J

2014-03-01

Immediately recalling a witnessed event can increase people's susceptibility to later postevent misinformation. But this retrieval-enhanced suggestibility (RES) effect has been shown only when the initial recall test included specific questions that reappeared on the final test. Moreover, it is unclear whether this phenomenon is affected by the centrality of event details. These limitations make it difficult to generalize RES to criminal investigations, which often begin with free recall prior to more specific queries from legal officials and attorneys. In 3 experiments, we examined the influence of test formats (free recall vs. cued recall) and centrality of event details (central vs. peripheral) on RES. In Experiment 1, both the initial and final tests were cued recall. In Experiment 2, the initial test was free recall and the final test was cued recall. In Experiment 3, both the initial and final tests were free recall. Initial testing increased misinformation reporting on the final test for peripheral details in all experiments, but the effect was significant for central details only after aggregating the data from all 3 experiments. These results show that initial free recall can produce RES, and more broadly, that free recall can potentiate subsequent learning of complex prose materials. © 2013 American Psychological Association

High-performance recombinant protein production with Escherichia coli in continuously operated cascades of stirred-tank reactors.

PubMed

Schmideder, Andreas; Weuster-Botz, Dirk

2017-07-01

The microbial expression of intracellular, recombinant proteins in continuous bioprocesses suffers from low product concentrations. Hence, a process for the intracellular production of photoactivatable mCherry with Escherichia coli in a continuously operated cascade of two stirred-tank reactors was established to separate biomass formation (first reactor) and protein expression (second reactor) spatially. Cascades of miniaturized stirred-tank reactors were implemented, which enable the 24-fold parallel characterization of cascade processes and the direct scale-up of results to the liter scale. With PAmCherry concentrations of 1.15 g L -1 cascades of stirred-tank reactors improved the process performance significantly compared to production processes in chemostats. In addition, an optimized fed-batch process was outperformed regarding space-time yield (149 mg L -1  h -1 ). This study implicates continuous cascade processes to be a promising alternative to fed-batch processes for microbial protein production and demonstrates that miniaturized stirred-tank reactors can reduce the timeline and costs for cascade process characterization.

The Population Biology of Bacterial Plasmids: A PRIORI Conditions for the Existence of Conjugationally Transmitted Factors

PubMed Central

Stewart, Frank M.; Levin, Bruce R.

1977-01-01

A mathematical model for the population dynamics of conjugationally transmitted plasmids in bacterial populations is presented and its properties analyzed. Consideration is given to nonbacteriocinogenic factors that are incapable of incorporation into the chromosome of their host cells, and to bacterial populations maintained in either continuous (chemostat) or discrete (serial transfer) culture. The conditions for the establishment and maintenance of these infectious extrachromosomal elements and equilibrium frequencies of cells carrying them are presented for different values of the biological parameters: population growth functions, conjugational transfer and segregation rate constants. With these parameters in a biologically realistic range, the theory predicts a broad set of physical conditions, resource concentrations and dilution rates, where conjugationally transmitted plasmids can become established and where cells carrying them will maintain high frequencies in bacterial populations. This can occur even when plasmid-bearing cells are much less fit (i.e., have substantially lower growth rates) than cells free of these factors. The implications of these results and the reality and limitations of the model are discussed and the values of its parameters in natural populations speculated upon. PMID:17248761

Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations

PubMed Central

Schreiber, Frank; Dal Co, Alma; Kiviet, Daniel J.; Littmann, Sten

2017-01-01

While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed. PMID:29253903

Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

PubMed Central

Fitzgerald, Colin M.; Camejo, Pamela; Oshlag, J. Zachary; Noguera, Daniel R.

2015-01-01

Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions. PMID:25506762

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

PubMed

Borirak, Orawan; Rolfe, Matthew D; de Koning, Leo J; Hoefsloot, Huub C J; Bekker, Martijn; Dekker, Henk L; Roseboom, Winfried; Green, Jeffrey; de Koster, Chris G; Hellingwerf, Klaas J

2015-10-01

Time-series transcript- and protein-profiles were measured upon initiation of carbon catabolite repression in Escherichia coli, in order to investigate the extent of post-transcriptional control in this prototypical response. A glucose-limited chemostat culture was used as the CCR-free reference condition. Stopping the pump and simultaneously adding a pulse of glucose, that saturated the cells for at least 1h, was used to initiate the glucose response. Samples were collected and subjected to quantitative time-series analysis of both the transcriptome (using microarray analysis) and the proteome (through a combination of 15N-metabolic labeling and mass spectrometry). Changes in the transcriptome and corresponding proteome were analyzed using statistical procedures designed specifically for time-series data. By comparison of the two sets of data, a total of 96 genes were identified that are post-transcriptionally regulated. This gene list provides candidates for future in-depth investigation of the molecular mechanisms involved in post-transcriptional regulation during carbon catabolite repression in E. coli, like the involvement of small RNAs. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Production and characterization of biodiesel from carbon dioxide concentrating chemolithotrophic bacteria, Serratia sp. ISTD04.

PubMed

Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

2014-02-01

A chemolithotrophic bacterium, Serratia sp. ISTD04, enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was evaluated for potential of carbon dioxide (CO2) sequestration and biofuel production. CO2 sequestration efficiency of the bacterium was determined by enzymatic activity of carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Further, Western blot analysis confirmed presence of RuBisCO. The bacterium produced 0.487 and 0.647mgmg(-1) per unit cell dry weight of hydrocarbons and lipids respectively. The hydrocarbons were within the range of C13-C24 making it equivalent to light oil. GC-MS analysis of lipids produced by the bacterium indicated presence of C15-C20 organic compounds that made it potential source of biodiesel after transesterification. GC-MS, FTIR and NMR spectroscopic characterization of the fatty acid methyl esters revealed the presence of 55% and 45% of unsaturated and saturated organic compounds respectively, thus making it a balanced biodiesel composition. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cloning and expression of gamma carbonic anhydrase from Serratia sp. ISTD04 for sequestration of carbon dioxide and formation of calcite.

PubMed

Srivastava, Shaili; Bharti, Randhir Kumar; Verma, Praveen Kumar; Thakur, Indu Shekhar

2015-01-01

Bacterial strains isolated from marble mines rock and enriched in the chemostat culture with different concentrations of sodium bicarbonate. The enriched consortium had six bacterial isolates. One of bacterium isolate showed carbonic anhydrase (CA) activity by catalyzing the reversible hydration reaction of carbon dioxide to bicarbonate. The bacterium was identified as Serratia sp. by 16S rRNA sequence analysis. The carbonic anhydrase gene from Serratia sp. was found to be homologous with gamma carbonic anhydrase. The carbonic anhydrase gene was cloned in PET21b(+) and expressed it in recombinant Escherichia coli BL21 (DE3) with His-tag at the C-terminus. The recombinant protein was purified efficiently by using one-step nickel affinity chromatography. Expected size of carbonic anhydrase was approximately 29 kDa in SDS-PAGE gel. Recombinant carbonic anhydrase enzyme was used for biomineralization-based conversion of atmospheric CO2 into valuable calcite minerals. The calcification was confirmed by using XRD, FTIR, EDX and SEM analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impact of phosphate limitation on PHA production in a feast-famine process.

PubMed

Korkakaki, Emmanouela; van Loosdrecht, Mark C M; Kleerebezem, Robbert

2017-12-01

Double-limitation systems have shown to induce polyhydroxyalkanoates (PHA) production in chemostat studies limited in e.g. carbon and phosphate. In this work the impact of double substrate limitation on the enrichment of a PHA producing community was studied in a sequencing batch process. Enrichments at different C/P concentration ratios in the influent were established and the effect on the PHA production capacity and the enrichment community structure was investigated. Experimental results demonstrated that when a double substrate limitation is imposed at a C/P ratio in the influent in a range of 150 (C-mol/mol), the P-content of the biomass and the specific substrate uptake rates decreased. Nonetheless, the PHA storage capacity remained high (with a maximum of 84 wt%). At a C/P ratio of 300, competition in the microbial community is based on phosphate uptake, and the PHA production capacity is lost. Biomass specific substrate uptake rates are a linear function of the cellular P-content, offering advantages for scaling-up the PHA production process due to lower oxygen requirements. Copyright © 2017 Elsevier Ltd. All rights reserved.

A simple strategy for in situ fabrication of a smart hydrogel microvalve within microchannels for thermostatic control.

PubMed

Lin, Shuo; Wang, Wei; Ju, Xiao-Jie; Xie, Rui; Chu, Liang-Yin

2014-08-07

Self-regulation of temperature in microchip systems is crucial for their applications in biomedical fields such as cell culture and biomolecule synthesis as well as those cases that require constant temperature conditions. Here we report on a simple and versatile approach for in situ fabrication of a smart hydrogel microvalve within a microchip for thermostatic control. The thermo-responsive hydrogel microvalve enables the "on-off" switch by sensing temperature fluctuations to control the fluid flux as well as the fluid heat exchange for self-regulation of the temperature at a constant range. Such temperature self-regulation is demonstrated by integrating the microvalve-incorporated microchip into the flow circulation loop of a micro-heat-exchanging system for thermostatic control. Moreover, the microvalve-incorporated microchip is employed for culturing cells under temperature self-regulation. The smart microvalve shows great potential as a temperature controller for applications that require thermostatic conditions. This approach offers a facile and flexible strategy for in situ fabricating hydrogel microvalves within microchips as chemostats and microreactors for biomedical applications.

Proteome analysis of yeast response to various nutrient limitations

PubMed Central

Kolkman, Annemieke; Daran-Lapujade, Pascale; Fullaondo, Asier; Olsthoorn, Maurien M A; Pronk, Jack T; Slijper, Monique; Heck, Albert J R

2006-01-01

We compared the response of Saccharomyces cerevisiae to carbon (glucose) and nitrogen (ammonia) limitation in chemostat cultivation at the proteome level. Protein levels were differentially quantified using unlabeled and 15N metabolically labeled yeast cultures. A total of 928 proteins covering a wide range of isoelectric points, molecular weights and subcellular localizations were identified. Stringent statistical analysis identified 51 proteins upregulated in response to glucose limitation and 51 upregulated in response to ammonia limitation. Under glucose limitation, typical glucose-repressed genes encoding proteins involved in alternative carbon source utilization, fatty acids β-oxidation and oxidative phosphorylation displayed an increased protein level. Proteins upregulated in response to nitrogen limitation were mostly involved in scavenging of alternative nitrogen sources and protein degradation. Comparison of transcript and protein levels clearly showed that upregulation in response to glucose limitation was mainly transcriptionally controlled, whereas upregulation in response to nitrogen limitation was essentially controlled at the post-transcriptional level by increased translational efficiency and/or decreased protein degradation. These observations underline the need for multilevel analysis in yeast systems biology. PMID:16738570

Microbial conversion of synthetic and food waste-derived volatile fatty acids to lipids.

PubMed

Vajpeyi, Shashwat; Chandran, Kartik

2015-01-01

Lipid accumulation in the oleaginous yeast Cryptococcus albidus was evaluated using mixtures of volatile fatty acids (VFA) as substrates. In general, batch growth under nitrogen limitation led to higher lipid accumulation using synthetic VFA. During batch growth, an initial COD:N ratio of 25:1mg COD:mg N led to maximum intracellular lipid accumulation (28.3 ± 0.7% g/g dry cell weight), which is the maximum reported for C. albidus using VFA as the carbon source, without compromising growth kinetics. At this feed COD:N ratio, chemostat cultures fed with synthetic VFA yielded statistically similar intracellular lipid content as batch cultures (29.9 ± 1.9%, g/g). However, batch cultures fed with VFA produced from the fermentation of food waste, yielded a lower lipid content (14.9 ± 0.1%, g/g). The lipid composition obtained with synthetic and food-waste-derived VFA was similar to commercial biodiesel feedstock. We therefore demonstrate the feasibility of linking biochemical waste treatment and biofuel production using VFA as key intermediates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Need-based activation of ammonium uptake in Escherichia coli

PubMed Central

Kim, Minsu; Zhang, Zhongge; Okano, Hiroyuki; Yan, Dalai; Groisman, Alexander; Hwa, Terence

2012-01-01

The efficient sequestration of nutrients is vital for the growth and survival of microorganisms. Some nutrients, such as CO2 and NH3, are readily diffusible across the cell membrane. The large membrane permeability of these nutrients obviates the need of transporters when the ambient level is high. When the ambient level is low, however, maintaining a high intracellular nutrient level against passive back diffusion is both challenging and costly. Here, we study the delicate management of ammonium (NH4+/NH3) sequestration by E. coli cells using microfluidic chemostats. We find that as the ambient ammonium concentration is reduced, E. coli cells first maximize their ability to assimilate the gaseous NH3 diffusing into the cytoplasm and then abruptly activate ammonium transport. The onset of transport varies under different growth conditions, but always occurring just as needed to maintain growth. Quantitative modeling of known interactions reveals an integral feedback mechanism by which this need-based uptake strategy is implemented. This novel strategy ensures that the expensive cost of upholding the internal ammonium concentration against back diffusion is kept at a minimum. PMID:23010999

Metabolic regulation of yeast

NASA Astrophysics Data System (ADS)

Fiechter, A.

1982-12-01

Metabolic regulation which is based on endogeneous and exogeneous process variables which may act constantly or time dependently on the living cell is discussed. The observed phenomena of the regulation are the result of physical, chemical, and biological parameters. These parameters are identified. Ethanol is accumulated as an intermediate product and the synthesis of biomass is reduced. This regulatory effect of glucose is used for the aerobic production of ethanol. Very high production rates are thereby obtained. Understanding of the regulation mechanism of the glucose effect has improved. In addition to catabolite repression, several other mechanisms of enzyme regulation have been described, that are mostly governed by exogeneous factors. Glucose also affects the control of respiration in a third class of yeasts which are unable to make use of ethanol as a substrate for growth. This is due to the lack of any anaplerotic activity. As a consequence, diauxic growth behavior is reduced to a one-stage growth with a drastically reduced cell yield. The pulse chemostat technique, a systematic approach for medium design is developed and medium supplements that are essential for metabolic control are identified.

Synchronized growth and neutral lipid accumulation in Chlorella sorokiniana FC6 IITG under continuous mode of operation.

PubMed

Kumar, Vikram; Muthuraj, Muthusivaramapandian; Palabhanvi, Basavaraj; Das, Debasish

2016-01-01

Synchronized growth and neutral lipid accumulation with high lipid productivity under mixotrophic growth of the strain Chlorella sorokiniana FC6 IITG was achieved via manipulation of substrates feeding mode and supplementation of lipid elicitors in the growth medium. Screening and optimization of lipid elicitors resulted in lipid productivity of 110.59mgL(-1)day(-1) under the combined effect of lipid inducers sodium acetate and sodium chloride. Fed-batch cultivation of the strain in bioreactor with intermittent feeding of limiting nutrients and lipid inducer resulted in maximum biomass and lipid productivity of 2.08 and 0.97gL(-1)day(-1) respectively. Further, continuous production of biomass with concomitant lipid accumulation was demonstrated via continuous feeding of BG11 media supplemented with lipid inducers sodium acetate and sodium chloride. The improved biomass and lipid productivity in chemostat was found to be 2.81 and 1.27gL(-1)day(-1) respectively operated at a dilution rate of 0.54day(-1). Copyright © 2015 Elsevier Ltd. All rights reserved.

The testing effect for mediator final test cues and related final test cues in online and laboratory experiments.

PubMed

Coppens, Leonora C; Verkoeijen, Peter P J L; Bouwmeester, Samantha; Rikers, Remy M J P

2016-05-31

The testing effect is the finding that information that is retrieved during learning is more often correctly retrieved on a final test than information that is restudied. According to the semantic mediator hypothesis the testing effect arises because retrieval practice of cue-target pairs (mother-child) activates semantically related mediators (father) more than restudying. Hence, the mediator-target (father-child) association should be stronger for retrieved than restudied pairs. Indeed, Carpenter (2011) found a larger testing effect when participants received mediators (father) than when they received target-related words (birth) as final test cues. The present study started as an attempt to test an alternative account of Carpenter's results. However, it turned into a series of conceptual (Experiment 1) and direct (Experiment 2 and 3) replications conducted with online samples. The results of these online replications were compared with those of similar existing laboratory experiments through small-scale meta-analyses. The results showed that (1) the magnitude of the raw mediator testing effect advantage is comparable for online and laboratory experiments, (2) in both online and laboratory experiments the magnitude of the raw mediator testing effect advantage is smaller than in Carpenter's original experiment, and (3) the testing effect for related cues varies considerably between online experiments. The variability in the testing effect for related cues in online experiments could point toward moderators of the related cue short-term testing effect. The raw mediator testing effect advantage is smaller than in Carpenter's original experiment.

The Education of Attention as Explanation of Variability of Practice Effects : Learning the Final Approach Phase in a Flight Simulator

ERIC Educational Resources Information Center

Huet, Michael; Jacobs, David M.; Camachon, Cyril; Missenard, Olivier; Gray, Rob; Montagne, Gilles

2011-01-01

The present study reports two experiments in which a total of 20 participants without prior flight experience practiced the final approach phase in a fixed-base simulator. All participants received self-controlled concurrent feedback during 180 practice trials. Experiment 1 shows that participants learn more quickly under variable practice…

Can Concentration - Discharge Relationships Diagnose Material Source During Extreme Events?

NASA Astrophysics Data System (ADS)

Karwan, D. L.; Godsey, S.; Rose, L.

2017-12-01

Floods can carry >90% of the basin material exported in a given year as well as alter flow pathways and material sources. In turn, sediment and solute fluxes can increase flood damages and negatively impact water quality and integrate physical and chemical weathering of landscapes and channels. Concentration-discharge (C-Q) relationships are used to both describe export patterns as well as compute them. Metrics for describing C-Q patterns and inferring their controls are vulnerable to infrequent sampling that affects how C-Q relationships are interpolated and interpreted. C-Q relationships are typically evaluated from multiple samples, but because hydrological extremes are rare, data are often unavailable for extreme events. Because solute and sediment C-Q relationships likely respond to changes in hydrologic extremes in different ways, there is a pressing need to define their behavior under extreme conditions, including how to properly sample to capture these patterns. In the absence of such knowledge, improving load estimates in extreme floods will likely remain difficult. Here we explore the use of C-Q relationships to determine when an event alters a watershed system such that it enters a new material source/transport regime. We focus on watersheds with sediment and discharge time series include low-frequency and/or extreme events. For example, we compare solute and sediment patterns in White Clay Creek in southeastern Pennsylvania across a range of flows inclusive of multiple hurricanes for which we have ample ancillary hydrochemical data. TSS is consistently mobilized during high flow events, even during extreme floods associated with hurricanes, and sediment fingerprinting indicates different sediment sources, including in-channel remobilization and landscape erosion, are active at different times. In other words, TSS mobilization in C-Q space is not sensitive to the source of material being mobilized. Unlike sediments, weathering solutes in this watershed tend to exhibit a relatively chemostatic C-Q pattern, except during the runoff-dominated Hurricane Irene, when they exhibit a diluting C-Q pattern. Finally, we summarize the vulnerability of these observations to shifts in sampling effort to highlight the utility and limitations of C-Q-derived export patterns.

The 30/20 GHz flight experiment system, phase 2. Volume 2: Experiment system description

NASA Technical Reports Server (NTRS)

Bronstein, L.; Kawamoto, Y.; Ribarich, J. J.; Scope, J. R.; Forman, B. J.; Bergman, S. G.; Reisenfeld, S.

1981-01-01

A detailed technical description of the 30/20 GHz flight experiment system is presented. The overall communication system is described with performance analyses, communication operations, and experiment plans. Hardware descriptions of the payload are given with the tradeoff studies that led to the final design. The spacecraft bus which carries the payload is discussed and its interface with the launch vehicle system is described. Finally, the hardwares and the operations of the terrestrial segment are presented.

Efficacy of surotomycin in an in vitro gut model of Clostridium difficile infection.

PubMed

Chilton, C H; Crowther, G S; Todhunter, S L; Nicholson, S; Freeman, J; Chesnel, L; Wilcox, M H

2014-09-01

We investigated the efficacy of the cyclic lipopeptide surotomycin in treating clindamycin-induced Clostridium difficile infection (CDI) using an in vitro gut model. Two three-stage chemostat gut models were inoculated with human faeces, spiked with C. difficile spores (∼10(7) cfu/mL, PCR ribotype 027 or 001). Clindamycin (33.9 mg/L, four times daily for 7 days) was dosed to induce CDI. Following high-level toxin production, surotomycin (250 mg/L, twice daily for 7 days) was instilled. Microflora populations, C. difficile vegetative cells and spores, cytotoxin titres and antimicrobial levels (LC-MS/MS and bioassay) were determined. The emergence of C. difficile and enterococci with reduced susceptibility to surotomycin was monitored on breakpoint agar (4 × MIC). Counts of viable C. difficile were reduced to near the limit of detection on Days 1 and 3 of surotomycin instillation, and cytotoxin was undetectable on Days 3 and 4 of surotomycin instillation in the 027 and 001 models, respectively. Recurrence of vegetative growth and toxin production occurred 11 days (001 model) and 15 days (027 model) after surotomycin instillation had ceased, and remained for the duration of the experiment. Surotomycin instillation decreased populations of bifidobacteria, clostridia, enterococci and lactobacilli, but was sparing of Bacteroides fragilis group populations. All enumerated organisms had recovered to steady-state levels by 3 weeks post-surotomycin instillation. No evidence of the emergence of reduced susceptibility to surotomycin was observed. Surotomycin successfully reduced C. difficile vegetative cell counts and toxin levels in the gut model and was sparing of B. fragilis group populations. There was no evidence of decreased susceptibility to surotomycin during exposure or post-exposure. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Bacterial growth and substrate degradation by BTX-oxidizing culture in response to salt stress.

PubMed

Lee, Chi-Yuan; Lin, Ching-Hsing

2006-01-01

Interactions between microbial growth and substrate degradation are important in determining the performance of trickle-bed bioreactors (TBB), especially when salt is added to reduce biomass formation in order to alleviate media clogging. This study was aimed at quantifying salinity effects on bacterial growth and substrate degradation, and at acquiring kinetic information in order to improve the design and operation of TBB. Experiment works began by cultivating a mixed culture in a chemostat reactor receiving artificial influent containing a mixture of benzene, toluene, and xylene (BTX), followed by using the enrichment culture to degrade the individual BTX substrates under a particular salinity, which ranged 0-50 g l(-1) in batch mode. Then, the measured concentrations of biomass and residual substrate versus time were analyzed with the microbial kinetics; moreover, the obtained microbial kinetic constants under various salinities were modeled using noncompetitive inhibition kinetics. For the three substrates the observed bacterial yields appeared to be decreased from 0.51-0.74 to 0.20-0.22 mg mg(-1) and the maximum specific rate of substrate utilization, q, declined from 0.25-0.42 to 0.07-0.11 h(-1), as the salinity increased from 0 to 50 NaCl g l(-1). The NaCl acted as noncompetitive inhibitor, where the modeling inhibitions of the coefficients, K ( T(S)), were 22.7-29.7 g l(-1) for substrate degradation and K ( T(mu)), 13.0-19.0 g l(-1), for biomass formation. The calculated ratios for the bacterial maintenance rate, m (S), to q, further indicated that the percentage energy spent on maintenance increased from 19-24 to 86-91% as salinity level increased from 0 to 50 g l(-1). These results revealed that the bacterial growth was more inhibited than substrate degradation by the BTX oxidizers under the tested salinity levels. The findings from this study demonstrate the potential of applying NaCl salt to control excessive biomass formation in biotrickling filters.

Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3−/NO2− reduction pathways in Shewanella loihica strain PV-4

PubMed Central

Yoon, Sukhwan; Cruz-García, Claribel; Sanford, Robert; Ritalahti, Kirsti M; Löffler, Frank E

2015-01-01

Denitrification and respiratory ammonification are two competing, energy-conserving NO3−/NO2− reduction pathways that have major biogeochemical consequences for N retention, plant growth and climate. Batch and continuous culture experiments using Shewanella loihica strain PV-4, a bacterium possessing both the denitrification and respiratory ammonification pathways, revealed factors that determine NO3−/NO2− fate. Denitrification dominated at low carbon-to-nitrogen (C/N) ratios (that is, electron donor-limiting growth conditions), whereas ammonium was the predominant product at high C/N ratios (that is, electron acceptor-limiting growth conditions). pH and temperature also affected NO3−/NO2− fate, and incubation above pH 7.0 and temperatures of 30 °C favored ammonium formation. Reverse-transcriptase real-time quantitative PCR analyses correlated the phenotypic observations with nirK and nosZ transcript abundances that decreased up to 1600-fold and 27-fold, respectively, under conditions favoring respiratory ammonification. Of the two nrfA genes encoded on the strain PV-4 genome, nrfA0844 transcription decreased only when the chemostat reactor received medium with the lowest C/N ratio of 1.5, whereas nrfA0505 transcription occurred at low levels (≤3.4 × 10−2 transcripts per cell) under all growth conditions. At intermediate C/N ratios, denitrification and respiratory ammonification occurred concomitantly, and both nrfA0844 (5.5 transcripts per cell) and nirK (0.88 transcripts per cell) were transcribed. Recent findings suggest that organisms with both the denitrification and respiratory ammonification pathways are not uncommon in soil and sediment ecosystems, and strain PV-4 offers a tractable experimental system to explore regulation of dissimilatory NO3−/NO2− reduction pathways. PMID:25350157

Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs.

PubMed

Lu, Hongzhong; Cao, Weiqiang; Ouyang, Liming; Xia, Jianye; Huang, Mingzhi; Chu, Ju; Zhuang, Yingping; Zhang, Siliang; Noorman, Henk

2017-03-01

Aspergillus niger is one of the most important cell factories for industrial enzymes and organic acids production. A comprehensive genome-scale metabolic network model (GSMM) with high quality is crucial for efficient strain improvement and process optimization. The lack of accurate reaction equations and gene-protein-reaction associations (GPRs) in the current best model of A. niger named GSMM iMA871, however, limits its application scope. To overcome these limitations, we updated the A. niger GSMM by combining the latest genome annotation and literature mining technology. Compared with iMA871, the number of reactions in iHL1210 was increased from 1,380 to 1,764, and the number of unique ORFs from 871 to 1,210. With the aid of our transcriptomics analysis, the existence of 63% ORFs and 68% reactions in iHL1210 can be verified when glucose was used as the only carbon source. Physiological data from chemostat cultivations, 13 C-labeled and molecular experiments from the published literature were further used to check the performance of iHL1210. The average correlation coefficients between the predicted fluxes and estimated fluxes from 13 C-labeling data were sufficiently high (above 0.89) and the prediction of cell growth on most of the reported carbon and nitrogen sources was consistent. Using the updated genome-scale model, we evaluated gene essentiality on synthetic and yeast extract medium, as well as the effects of NADPH supply on glucoamylase production in A. niger. In summary, the new A. niger GSMM iHL1210 contains significant improvements with respect to the metabolic coverage and prediction performance, which paves the way for systematic metabolic engineering of A. niger. Biotechnol. Bioeng. 2017;114: 685-695. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Biofilms promote altruism.

PubMed

Kreft, Jan-Ulrich

2004-08-01

The origin of altruism is a fundamental problem in evolution, and the maintenance of biodiversity is a fundamental problem in ecology. These two problems combine with the fundamental microbiological question of whether it is always advantageous for a unicellular organism to grow as fast as possible. The common basis for these three themes is a trade-off between growth rate and growth yield, which in turn is based on irreversible thermodynamics. The trade-off creates an evolutionary alternative between two strategies: high growth yield at low growth rate versus high growth rate at low growth yield. High growth yield at low growth rate is a case of an altruistic strategy because it increases the fitness of the group by using resources economically at the cost of decreased fitness, or growth rate, of the individual. The group-beneficial behaviour is advantageous in the long term, whereas the high growth rate strategy is advantageous in the short term. Coexistence of species requires differences between their niches, and niche space is typically divided into four 'axes' (time, space, resources, predators). This neglects survival strategies based on cooperation, which extend the possibilities of coexistence, arguing for the inclusion of cooperation as the fifth 'axis'. Here, individual-based model simulations show that spatial structure, as in, for example, biofilms, is necessary for the origin and maintenance of this 'primitive' altruistic strategy and that the common belief that growth rate but not yield decides the outcome of competition is based on chemostat models and experiments. This evolutionary perspective on life in biofilms can explain long-known biofilm characteristics, such as the structural organization into microcolonies, the often-observed lack of mixing among microcolonies, and the shedding of single cells, as promoting the origin and maintenance of the altruistic strategy. Whereas biofilms enrich altruists, enrichment cultures, microbiology's paradigm for isolating bacteria into pure culture, select for highest growth rate.

NASA In-step: Permeable Membrane Experiment

NASA Technical Reports Server (NTRS)

1992-01-01

Viewgraphs on the Permeable Membrane Experiment are presented. An experiment overview is given. The Membrane Phase Separation Experiment, Membrane Diffusion Interference Experiment, and Membrane Wetting Experiment are described. Finally, summary and conclusions are discussed.

Military Experience Directed into Health Careers. Final Report.

ERIC Educational Resources Information Center

Health Research and Educational Fund of New Jersey, Princeton, NJ.

Operation MEDIHC's (Military Experience Directed into Health Careers) final report is presented which firmly establishes the need for its purpose, which is providing a meaningful career continuation for medical personnel who were trained while serving in the military service. It is reported that the New Jersey MEDIHC Program experienced a…

Interaction Between Syntactic Structure and Information Structure in the Processing of a Head-Final Language.

PubMed

Koizumi, Masatoshi; Imamura, Satoshi

2017-02-01

The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two factors is not restricted to head-initial languages. The second experiment revealed that the interaction between syntactic structure and information structure occurs at the second NP (O of SOV and S of OSV), which, crucially, is a pre-head position, suggesting the incremental nature of the processing of both syntactic structure and information structure in head-final languages.

Students' Experiences of Clinic-Based Learning during a Final Year Veterinary Internship Programme

ERIC Educational Resources Information Center

Matthew, Susan M.; Taylor, Rosanne M.; Ellis, Robert A.

2010-01-01

This study investigated veterinary students' experiences of clinic-based learning (CBL) during a comprehensive final year internship programme. Open-ended surveys (n = 93) were used to gather qualitative data about students' conceptions of what is learned during CBL and their approaches to learning in clinics. Phenomenography was used for detailed…

DoE Early Career Research Program: Final Report: Model-Independent Dark-Matter Searches at the ATLAS Experiment and Applications of Many-core Computing to High Energy Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farbin, Amir

2015-07-15

This is the final report of for DoE Early Career Research Program Grant Titled "Model-Independent Dark-Matter Searches at the ATLAS Experiment and Applications of Many-core Computing to High Energy Physics".

Influence of hydroclimatic variations on solute concentration dynamics in nested subtropical catchments with heterogeneous landscapes.

PubMed

Piazza, Gustavo Antonio; Dupas, Rémi; Gascuel-Odoux, Chantal; Grimaldi, Catherine; Pinheiro, Adilson; Kaufmann, Vander

2018-04-20

Despite global efforts to monitor water quality in catchments worldwide, tropical and subtropical zones still lack data to study the influence of human activities and climate variations on solute dynamics. In this study, we monitored ten solutes every two weeks for six years (2010-2015) in three nested catchments (2 to30 km 2 ), which contained heterogeneous landscapes composed of forests and agricultural land, and one small neighboring forested catchment (0.4 km 2 ). Data analysis revealed that i) rainfall, discharge and solute concentrations displayed no clear seasonal patterns, unlike many catchments of the temperate zone; ii) solute concentrations in the agricultural area were higher than those in the forested area, but both areas displayed similar temporal patterns due to a common hydroclimatic driver; iii) all four catchments displayed a chemostatic export regime for most of the solutes, similar to catchments of the temperate zone; and iv) a positive correlation was observed between anion concentrations and ENSO (El Niño-Southern Oscillation) index. ENSO appeared to influence both hydroclimatic and anion dynamics in these subtropical catchments. Copyright © 2018 Elsevier B.V. All rights reserved.

Effect of monoclonal antibodies against lipoteichoic acid from the oral bacterium Streptococcus mutans on its adhesion and plaque-accumulation in vitro.

PubMed

Stashenko, P; Peros, W J; Gibbons, R J; Dearborn, S M

1986-01-01

Five monoclonal antibodies directed against Streptococcus mutans strain JBP lipoteichoic acid (LTA) were characterized. They were all similarly reactive with the immunizing LTA-containing extract, with intact Strep. mutans JBP cells and with LTA purified from Lactobacillus casei. Immobilized anti-LTA antibodies removes LTA from LTA-containing extracts. The binding of antibodies to LTA was inhibited by the aqueous extract but not by the organic extract of de-acylated LTA, indicating reactivity with the polyglycerol-phosphate portion of the molecule. Antibodies were reactive with all serotypes of Strep. mutans, as well as with strains of Streptococcus salivarius, Streptococcus sanguis and L. casei, but not with LTA-negative species Streptococcus mitis or Actinomyces viscosus. Anti-LTA antibodies at doses of 0.3 or 3.0 micrograms/ml, had no effect on the adherence of Strep. mutans JBP to experimental salivary pellicles formed on hydroxyapatite, but enhanced adherence 150-300 per cent at 30 micrograms/ml. There was no effect of anti-LTA antibodies in a chemostat model which measured sucrose-dependent plaque accumulation by Strep. mutans. The results argue against a major role for LTA in Strep. mutans adherence or plaque accumulation in vitro.

The river as a chemostat: fresh perspectives on dissolved organic matter flowing down the river continuum

USGS Publications Warehouse

Creed, Irena F.; McKnight, Diane M.; Pellerin, Brian; Green, Mark B.; Bergamaschi, Brian; Aiken, George R.; Burns, Douglas A.; Findlay, Stuart E G; Shanley, James B.; Striegl, Robert G.; Aulenbach, Brent T.; Clow, David W.; Laudon, Hjalmar; McGlynn, Brian L.; McGuire, Kevin J.; Smith, Richard A.; Stackpoole, Sarah M.

2015-01-01

A better understanding is needed of how hydrological and biogeochemical processes control dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) composition from headwaters downstream to large rivers. We examined a large DOM dataset from the National Water Information System of the US Geological Survey, which represents approximately 100 000 measurements of DOC concentration and DOM composition at many sites along rivers across the United States. Application of quantile regression revealed a tendency towards downstream spatial and temporal homogenization of DOC concentrations and a shift from dominance of aromatic DOM in headwaters to more aliphatic DOM downstream. The DOC concentration–discharge (C-Q) relationships at each site revealed a downstream tendency towards a slope of zero. We propose that despite complexities in river networks that have driven many revisions to the River Continuum Concept, rivers show a tendency towards chemostasis (C-Q slope of zero) because of a downstream shift from a dominance of hydrologic drivers that connect terrestrial DOM sources to streams in the headwaters towards a dominance of instream and near-stream biogeochemical processes that result in preferential losses of aromatic DOM and preferential gains of aliphatic DOM.

The Possible Emergence of Life and Differentiation of a Shallow Biosphere on Irradiated Icy Worlds: The Example of Europa

NASA Astrophysics Data System (ADS)

Russell, Michael J.; Murray, Alison E.; Hand, Kevin P.

2017-12-01

Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs - relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts - could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms. In such chemostatic environments, fuels may eventually outweigh oxidants. Ice-covered oceans are primarily heated from below, creating convection that could transport putative microbial cells and cellular cooperatives upward to congregate beneath an ice shell, potentially giving rise to a highly focused shallow biosphere. It is here where electron acceptors, ultimately derived from the irradiated surface, could be delivered to such life-forms through exchange with the icy surface. Such zones would act as "electron disposal units" for the biosphere, and occupants might be transferred toward the surface by buoyant diapirs and even entrained into plumes.

Microbial degradation of hydrocarbons in the environment.

PubMed Central

Leahy, J G; Colwell, R R

1990-01-01

The ecology of hydrocarbon degradation by microbial populations in the natural environment is reviewed, emphasizing the physical, chemical, and biological factors that contribute to the biodegradation of petroleum and individual hydrocarbons. Rates of biodegradation depend greatly on the composition, state, and concentration of the oil or hydrocarbons, with dispersion and emulsification enhancing rates in aquatic systems and absorption by soil particulates being the key feature of terrestrial ecosystems. Temperature and oxygen and nutrient concentrations are important variables in both types of environments. Salinity and pressure may also affect biodegradation rates in some aquatic environments, and moisture and pH may limit biodegradation in soils. Hydrocarbons are degraded primarily by bacteria and fungi. Adaptation by prior exposure of microbial communities to hydrocarbons increases hydrocarbon degradation rates. Adaptation is brought about by selective enrichment of hydrocarbon-utilizing microorganisms and amplification of the pool of hydrocarbon-catabolizing genes. The latter phenomenon can now be monitored through the use of DNA probes. Increases in plasmid frequency may also be associated with genetic adaptation. Seeding to accelerate rates of biodegradation has been shown to be effective in some cases, particularly when used under controlled conditions, such as in fermentors or chemostats. PMID:2215423

Nutrient control of eukaryote cell growth: a systems biology study in yeast.

PubMed

Gutteridge, Alex; Pir, Pinar; Castrillo, Juan I; Charles, Philip D; Lilley, Kathryn S; Oliver, Stephen G

2010-05-24

To elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast, Saccharomyces cerevisiae, growing at a range of growth rates and in four different nutrient-limiting conditions. We find significant changes in expression for many genes in each of the four nutrient-limited conditions tested. We also observe several processes that respond differently to changes in growth rate and are specific to each nutrient-limiting condition. These include carbohydrate storage, mitochondrial function, ribosome synthesis, and phosphate transport. Integrating transcriptome data with proteome measurements allows us to identify previously unrecognized examples of post-transcriptional regulation in response to both nutrient and growth-rate signals. Our results emphasize the unique properties of carbon metabolism and the carbon substrate, the limitation of which induces significant changes in gene regulation at the transcriptional and post-transcriptional level, as well as altering how many genes respond to growth rate. By comparison, the responses to growth limitation by other nutrients involve a smaller set of genes that participate in specific pathways. See associated commentary http://www.biomedcentral.com/1741-7007/8/62.

Stoichiometry, Metabolism and Nutrient Limitation Across the Periodic Table in Natural Flowing-Water Chemostats

NASA Astrophysics Data System (ADS)

Cohen, M. J.; Nifong, R. L.; Kurz, M. J.; Cropper, W. P.; Martin, J. B.

2014-12-01

Relative supplies of macro and micronutrients (C,N,P, various metals), along with light and water, controls ecosystem metabolism, trophic energy transfer and community structure. Here we test the hypothesis, using measurements from 41 spring-fed rivers in Florida, that tissue stoichiometry indicates autotroph nutrient limitation status. Low variation in discharge, temperature and chemical composition within springs, but large variation across springs creates an ideal setting to assess the relationship between limitation and resource supply. Molar N:P ranges from 0.4 to 90, subjecting autotrophs to dramatically different nutrient supply. Over this gradient, species-specific autotroph tissue C:N:P ratios are strictly homeostatic, and with no evidence that nutrient supply affects species composition. Expanding to include 19 metals and micronutrients revealed autotrophs are more plastic in response to micronutrient variation, particularly for iron and manganese whose supply fluxes are small compared to biotic demand. Using a Droop model modified to reflect springs conditions (benthic production, light limitation, high hydraulic turnover), we show that tissue stoichiometry transitions from homeostatic to plastic with the onset of nutrient limitation, providing a potentially powerful new tool for predicting nutrient limitation and thus eutrophication in flowing waters.

The kinetic study of hydrogen bacteria and methanotrophs in pure and defined mixed cultures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arora, D.K.

The kinetics of pure and mixed cultures of Alcaligenes eutrophus H 16 and Methylobacterium organophilum CRL 26 under double substrate limited conditions were studied. In pure culture growth kinetics, a non-interactive model was found to fit the experimental data best. The yield of biomass on limiting substrate was found to vary with the dilution rate. The variation in the biomass yield may be attributed to the change in metabolic pathways resulting from a shift in the limiting substrates. Both species exhibited wall growth in the chemostat under dark conditions. However, under illuminated conditions, there was significant reduction in wall growth.more » Poly-{beta}-hydroxybutyric acid was synthesized by both species under ammonia and oxygen limiting conditions. The feed gas mixture was optimized to achieve the steady-state coexistence of these two species in a chemostate for the first time. In mixed cultures, the biomass species assays were differentiated on the basis of their selective growth on particular compounds: Sarcosine and D-arabinose were selected for hydrogen bacteria and methylotrophs, respectively. The kinetics parameters estimated from pure cultures were used to predict the growth kinetics of these species in defined mixed cultures.« less

Effect of flow and active mixing on bacterial growth in a colon-like geometry

NASA Astrophysics Data System (ADS)

Cremer, Jonas; Segota, Igor; Arnoldini, Markus; Groisman, Alex; Hwa, Terence

The large intestine harbors bacteria from hundreds of species, with bacterial densities reaching up to 1012 cells per gram. Many different factors influence bacterial growth dynamics and thus bacterial density and microbiota composition. One dominant force is flow which can in principle lead to a washout of bacteria from the proximal colon. Active mixing by Contractions of the colonic wall together with bacterial growth might counteract such flow-forces and allow high bacterial densities to occur. As a step towards understanding bacterial growth in the presence of mixing and flow, we constructed an in-vitro setup where controlled wall-deformations of a channel emulate Contractions. We investigate growth along the channel under a steady nutrient inflow. In the limits of no or very frequent Contractions, the device behaves like a plug-flow reactor and a chemostat respectively. Depending on mixing and flow, we observe varying spatial gradients in bacterial density along the channel. Active mixing by deformations of the channel wall is shown to be crucial in maintaining a steady-state bacterial population in the presence of flow. The growth-dynamics is quantitatively captured by a simple mathematical model, with the effect of mixing described by an effective diffusion term.

Biotechnological Applications of Microbial (Per)chlorate Reduction.

PubMed

Wang, Ouwei; Coates, John D

2017-11-24

While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration. This ability, along with other novel aspects of the metabolism, have resulted in a wide and disparate range of potential biotechnological applications being proposed, including enzymatic perchlorate detection; gas gangrene therapy; enhanced xenobiotic bioremediation; oil reservoir bio-souring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and, biogenic oxygen production for planetary exploration. While previous reviews focus on the fundamental science of microbial (per)chlorate reduction (for example see Youngblut et al., 2016), here, we provide an overview of the emerging biotechnological applications of (per)chlorate respiration and the underlying organisms and enzymes to environmental and biotechnological industries.

Experience-Based Career Education. High School Level Demonstration Project. Final Report (October 1, 1976 to July 30, 1979).

ERIC Educational Resources Information Center

Greenville County School District, Greenville, SC.

An Experience-Based Career Education (EBCE) exemplary project was conducted for three years in four high schools in Greenville County, South Carolina, and then evaluated for this final program report. Guidance and community components made up the program's major strengths. A third component (academic) proved nonessential. The guidance component…

Interaction between Syntactic Structure and Information Structure in the Processing of a Head-Final Language

ERIC Educational Resources Information Center

Koizumi, Masatoshi; Imamura, Satoshi

2017-01-01

The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two…

What Works Clearinghouse Quick Review: "Transfer Incentives for High-Performing Teachers: Final Results from a Multisite Experiment"

ERIC Educational Resources Information Center

What Works Clearinghouse, 2014

2014-01-01

"Transfer Incentives for High-Performing Teachers: Final Results from a Multisite Experiment," examined the impact of the Talent Transfer Initiative (TTI) on both student achievement and teacher retention in 10 school districts across seven states. The initiative gave bonuses to high-performing teachers for them to transfer to and stay…

Remote measurements of upper atmospheric density and temperature

NASA Technical Reports Server (NTRS)

Yee, Jeng-Hwa

1995-01-01

A suborbital experiment was designed to study the photochemistry of the mesosphere by observing simultaneously the airglow emissions with in-situ minor species number density profiles. The experiment was very successful and some preliminary results have already been reported in various scientific meetings. Two scientific papers are currently in the process of final preparation for submission for publication. In this final project report, we will first give a background description of the experiment and follow by the summaries of the scientific papers currently being prepared.

WWC Review of the Report "Transfer Incentives for High-Performing Teachers: Final Results from a Multisite Randomized Experiment." What Works Clearinghouse Single Study Review

ERIC Educational Resources Information Center

What Works Clearinghouse, 2015

2015-01-01

For the 2013 study, "Transfer Incentives for High-Performing Teachers: Final Results from a Multisite Randomized Experiment," researchers examined the impact of the Talent Transfer Initiative (TTI) on students' reading and mathematics achievement in 10 school districts. The TTI enabled principals of low-performing schools to provide…

Final Technical Report [Cosmogenic background and shielding R&D for a Ge Neutrinoless Double Beta Decay Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guiseppe, Vince

2013-10-01

The USD Majorana group focused all of its effort in support of the MAJORANA DEMONSTRATOR (MJD) experiment. Final designs of the shielding subsystems are complete. Construction of the MJD shielding systems at SURF has begun and the proposed activities directly support the completion of the shield systems. The PI and the group contribute heavily to the onsite construction activities of the MJD experiment. The group led investigations into neutron and neutron-­induced backgrounds, shielding effectiveness and design, and radon backgrounds.

Critique of "A Big Apple for Educators: New York City's Experiment with Schoolwide Performance Bonuses: Final Evaluation Report"

ERIC Educational Resources Information Center

Fallah, Soraya; Moradian, Cklara

2017-01-01

The purpose of this paper is to review and critique a groundbreaking research report. The research article under review in this paper is: "A Big Apple for Educators: New York City's Experiment with Schoolwide Performance Bonuses: Final Evaluation Report" (see ED521920). In 2007-08, a program called the Schoolwide Performance Bonus…

An Investigation of the Teacher Competencies Needed to Utilize Diagnostic Test Data in Prescribing Occupational Learning Experiences in Teaching EMRS. Final Report. Part II. Appendices.

ERIC Educational Resources Information Center

Nelson, Orville; And Others

These appendixes are to the final report of an action research Project conducted to determine the teacher competencies needed in order to develop valid and effective occupational learning experiences for educable mentally retarded (EMR) students based on available diagnostic test data and information. Included are (1) participant vitas and…

Study of Natural Fiber Breakage during Composite Processing

NASA Astrophysics Data System (ADS)

Quijano-Solis, Carlos Jafet

Biofiber-thermoplastic composites have gained considerable importance in the last century. To provide mechanical reinforcement to the polymer, fibers must be larger than a critical aspect ratio (length-to-width ratio). However, biofibers undergo breakage in length or width during processing, affecting their final aspect ratio in the composites. In this study, influence on biofiber breakage by factors related to processing conditions, fiber morphology and the flow type was investigated through: a) experiments using an internal mixer, a twin-screw extruder (TSE) or a capillary rheometer; and b) a Monte Carlo computer simulation. Composites of thermomechanical fibers of aspen or wheat straw mixed with polypropylene were studied. Internal mixer experiments analyzed wheat straw and two batches of aspen fibers, named AL and AS. AL fibers had longer average length. Processing variables included the temperature, rotors speed and fiber concentration. TSE experiments studied AL and AS fiber composites under various screws speeds, temperatures and feeding rates of the polymer and fibers. Capillary rheometers experiments determined AL fiber breakage in shear and elongational flows for composites processed at different concentrations, temperatures, and strain rates. Finally, the internal mixer experimental results where compared to Monte Carlo simulation predictions. The simulation focused on fiber length breakage due to fiber-polymer interactions. Internal mixer results showed that final fiber average length depended almost solely on processing conditions while final fiber average width depended on both processing conditions and initial fiber morphology. In the TSE, processing conditions as well as initial fiber length influenced final average length. TSE results showed that the fiber concentration regime seems to influence the effect of processing variables on fiber breakage. Capillary rheometer experiments demonstrated that biofiber breakage happens in both elongational and shear flows. In some cases, percentage of biofiber breakage in elongational flow is higher. In general, simulation predictions of final average lengths were in good agreement with experiments, indicating the importance of fiber-polymer interactions on fiber breakage. The largest discrepancies were obtained at higher fiber concentration composites; these differences might be resolved, in future simulations, by including the effect of fiber-fiber interactions.

The Costs and Benefits of Testing and Guessing on Recognition Memory

PubMed Central

Huff, Mark J.; Balota, David A.; Hutchison, Keith A.

2016-01-01

We examined whether two types of interpolated tasks (i.e., retrieval-practice via free recall or guessing a missing critical item) improved final recognition for related and unrelated word lists relative to restudying or completing a filler task. Both retrieval-practice and guessing tasks improved correct recognition relative to restudy and filler tasks, particularly when study lists were semantically related. However, both retrieval practice and guessing also generally inflated false recognition for the non-presented critical words. These patterns were found when final recognition was completed during a short delay within the same experimental session (Experiment 1) and following a 24-hr delay (Experiment 2). In Experiment 3, task instructions were presented randomly after each list to determine whether retrieval-practice and guessing effects were influenced by task-expectancy processes. In contrast to Experiments 1 and 2, final recognition following retrieval practice and guessing was equivalent to restudy, suggesting that the observed retrieval-practice and guessing advantages were in part due to preparatory task-based processing during study. PMID:26950490

48 CFR 1852.235-73 - Final Scientific and Technical Reports.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Final Scientific and Technical Reports. 1852.235-73 Section 1852.235-73 Federal Acquisition Regulations System NATIONAL..., including recommendations and conclusions based on the experience and results obtained. The final report...

Age, School Experience and the Development of Visual-Perceptual Memory. Final Report, Part 2.

ERIC Educational Resources Information Center

Goulet, L. R.

This study attempted to investigate the effects of school experience on visual perception tests involving line figures and forms. There were two experiments in this study. Experiment 1 examined the independent and interactive influences of school experience and chronological age in kindergarten children. Experiment 2 compared the effects of…

Does representational momentum reflect a distortion of the length or the endpoint of a trajectory?

PubMed

Hubbard, Timothy L; Motes, Michael A

2002-01-01

Observers viewed a moving target, and after the target vanished, indicated either the initial position or the final position of the target. In Experiment 1, an auditory tone cued observers to indicate either the initial position or the final position; in Experiment 2, different groups of observers indicated the initial position or the final position. Judgments of the initial position were displaced backward in the direction opposite to motion, and judgments of the final position were displaced forward in the direction of motion. The data suggest that the remembered trajectory is longer than the actual trajectory, and the displacement pattern is not consistent with the hypothesis that representational momentum results from a distortion of memory for the location of a trajectory.

Alloy undercooling experiments

NASA Technical Reports Server (NTRS)

Flemings, Merton C.; Matson, Douglas M.

1995-01-01

The research accomplished during 1995 can be organized into three parts. The first task involves analyzing the results of microgravity experiments carried out using TEMPUS hardware during the IML-2 mission on STS-65. The second part was to finalize ground-based experimentation which supported the above flight sample analysis. The final part was to provide technical support for post-flight mission activities specifically aimed at improving TEMPUS performance for potential future missions.

The performance assessment of undergraduate students in physics laboratory by using guided inquiry

NASA Astrophysics Data System (ADS)

Mubarok, H.; Lutfiyah, A.; Kholiq, A.; Suprapto, N.; Putri, N. P.

2018-03-01

The performance assessment of basic physics experiment among undergraduate physics students which includes three stages: pre-laboratory, conducting experiment and final report was explored in this study. The research used a descriptive quantitative approach by utilizing guidebook of basic physics experiment. The findings showed that (1) the performance of pre-laboratory rate among undergraduate physics students in good category (average score = 77.55), which includes the ability of undergraduate physics students’ theory before they were doing the experiment. (2) The performance of conducting experiment was in good category (average score = 78.33). (3) While the performance of final report was in moderate category (average score = 73.73), with the biggest weakness at how to analyse and to discuss the data and writing the abstract.

Surface Roughness Optimization Using Taguchi Method of High Speed End Milling For Hardened Steel D2

NASA Astrophysics Data System (ADS)

Hazza Faizi Al-Hazza, Muataz; Ibrahim, Nur Asmawiyah bt; Adesta, Erry T. Y.; Khan, Ahsan Ali; Abdullah Sidek, Atiah Bt.

2017-03-01

The main challenge for any manufacturer is to achieve higher quality of their final products with maintains minimum machining time. In this research final surface roughness analysed and optimized with maximum 0.3 mm flank wear length. The experiment was investigated the effect of cutting speed, feed rate and depth of cut on the final surface roughness using D2 as a work piece hardened to 52-56 HRC, and coated carbide as cutting tool with higher cutting speed 120-240 mm/min. The experiment has been conducted using L9 design of Taguchi collection. The results have been analysed using JMP software.

The Mini-Earth facility and present status of habitation experiment program.

PubMed

Nitta, Keiji

2005-01-01

The history of construction of the CEEF (the Mini-Earth), the configuration and scale of the CEEF are initially described. The effective usable areas in plant cultivation and animal holding and habitation modules and the accommodation equipment installed in each module are also explained. Mechanisms of the material circulation systems belonging to each module and subsystems in each material circulation system are introduced. Finally the results of pre-habitation experiments conducted until the year 2004 for clarifying the requirements in order to promote final closed habitation experiments are shown. c2005 Published by Elsevier Ltd on behalf of COSPAR.

Exploring Mathematics Teacher Education Fieldwork Experiences through Storytelling

ERIC Educational Resources Information Center

Elrod, Melody Jeane

2017-01-01

Throughout the history of teacher education, the final fieldwork experience has often been called the single most influential experience in teacher preparation programs (Burns, Jacobs, & Yendol-Hoppey, 2016; Feiman-Nemser & Buchmann, 1986; Parker-Katz & Bay, 2008). Though this experience has been expanded to include fieldwork…

Kinetics of Bacterial Growth on Chlorinated Aliphatic Compounds

PubMed Central

van den Wijngaard, Arjan J.; Wind, Richèle D.; Janssen, Dick B.

1993-01-01

With the pure bacterial cultures Ancylobacter aquaticus AD20 and AD25, Xanthobacter autotrophicus GJ10, and Pseudomonas sp. strain AD1, Monod kinetics was observed during growth in chemostat cultures on 1,2-dichloroethane (AD20, AD25, and GJ10), 2-chloroethanol (AD20 and GJ10), and 1,3-dichloro-2-propanol (AD1). Both the Michaelis-Menten constants (Km) of the first catabolic (dehalogenating) enzyme and the Monod half-saturation constants (Ks) followed the order 2-chloroethanol, 1,3-dichloro-2-propanol, epichlorohydrin, and 1,2-dichloroethane. The Ks values of strains GJ10, AD20, and AD25 for 1,2-dichloroethane were 260, 222, and 24 μM, respectively. The low Ks value of strain AD25 was correlated with a higher haloalkane dehalogenase content of this bacterium. The growth rates of strains AD20 and GJ10 in continuous cultures on 1,2-dichloroethane were higher than the rates predicted from the kinetics of the haloalkane dehalogenase and the concentration of the enzyme in the cells. The results indicate that the efficiency of chlorinated compound removal is indeed influenced by the kinetic properties and cellular content of the first catabolic enzyme. The cell envelope did not seem to act as a barrier for permeation of 1,2-dichloroethane. PMID:16348981

The Possible Emergence of Life and Differentiation of a Shallow Biosphere on Irradiated Icy Worlds: The Example of Europa.

PubMed

Russell, Michael J; Murray, Alison E; Hand, Kevin P

2017-12-01

Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs-relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts-could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms. In such chemostatic environments, fuels may eventually outweigh oxidants. Ice-covered oceans are primarily heated from below, creating convection that could transport putative microbial cells and cellular cooperatives upward to congregate beneath an ice shell, potentially giving rise to a highly focused shallow biosphere. It is here where electron acceptors, ultimately derived from the irradiated surface, could be delivered to such life-forms through exchange with the icy surface. Such zones would act as "electron disposal units" for the biosphere, and occupants might be transferred toward the surface by buoyant diapirs and even entrained into plumes. Key Words: Biofilms-Europa-Extraterrestrial life-Hydrothermal systems. Astrobiology 17, 1265-1273.

The Possible Emergence of Life and Differentiation of a Shallow Biosphere on Irradiated Icy Worlds: The Example of Europa

PubMed Central

Murray, Alison E.; Hand, Kevin P.

2017-01-01

Abstract Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs—relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts—could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms. In such chemostatic environments, fuels may eventually outweigh oxidants. Ice-covered oceans are primarily heated from below, creating convection that could transport putative microbial cells and cellular cooperatives upward to congregate beneath an ice shell, potentially giving rise to a highly focused shallow biosphere. It is here where electron acceptors, ultimately derived from the irradiated surface, could be delivered to such life-forms through exchange with the icy surface. Such zones would act as “electron disposal units” for the biosphere, and occupants might be transferred toward the surface by buoyant diapirs and even entrained into plumes. Key Words: Biofilms—Europa—Extraterrestrial life—Hydrothermal systems. Astrobiology 17, 1265–1273. PMID:29016193

Fueling the caries process: carbohydrate metabolism and gene regulation by Streptococcus mutans

PubMed Central

Moye, Zachary D.; Zeng, Lin; Burne, Robert A.

2014-01-01

The nature of the oral cavity and host behaviors has mandated that the oral microbiota evolve mechanisms for coping with environmental fluctuations, especially changes in the type and availability of carbohydrates. In the case of human dental caries, the presence of excess carbohydrates is often responsible for altering the local environment to be more favorable for species associated with the initiation and progression of disease, including Streptococcus mutans. Some of the earliest endeavors to understand how cariogenic species respond to environmental perturbations were carried out using chemostat cultivation, which provides fine control over culture conditions and bacterial behaviors. The development of genome-scale methodologies has allowed for the combination of sophisticated cultivation technologies with genome-level analysis to more thoroughly probe how bacterial pathogens respond to environmental stimuli. Recent investigations in S. mutans and other closely related streptococci have begun to reveal that carbohydrate metabolism can drastically impact pathogenic potential and highlight the important influence that nutrient acquisition has on the success of pathogens; inside and outside of the oral cavity. Collectively, research into pathogenic streptococci, which have evolved in close association with the human host, has begun to unveil the essential nature of careful orchestration of carbohydrate acquisition and catabolism to allow the organisms to persist and, when conditions allow, initiate or worsen disease. PMID:25317251

Differential evolution of asexual and sexual females in a benign culture environment

PubMed Central

Snell, Terry W.

2013-01-01

Here we report one of the first investigations of evolvability of lifespan and reproduction in metazoans, examining both extrinsic and intrinsic factors. We tested effects on senescence of an environmental variable (simulated lake hydroperiod, the length of time an aquatic habitat is inundated), female reproductive physiology (asexual females that reproduce by ameiosis, versus sexual females reproducing by meiosis), and time in a benign culture environment (minimal, if any, external mortality factors). To do this we established chemostat cultures of the rotifer Brachionus plicatilis s.s., and maintained the cultures for 385 d. Hydroperiod alone or in interaction with the effects of time in the benign environment (season) or reproductive physiology had no significant effect on the net reproductive rate, generation time, or rate of aging. Yet combining animals from both ephemeral and permanent hydroperiods revealed a 26% increase in asexual female lifespan across seasons (23% decrease in the rate of aging) and a 56% increase in asexual fecundity, suggesting that maintenance in benign laboratory conditions leads to slower aging. The relative stasis of traits for sexual females implies an impact of reproductive physiology on evolvability. In addition we found a positive correlation between fecundity and lifespan, suggesting an absence of trade-offs in life history traits in the benign laboratory environment. PMID:24795527

Intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease.

PubMed

Wang, Zi-Kai; Yang, Yun-Sheng; Chen, Ye; Yuan, Jing; Sun, Gang; Peng, Li-Hua

2014-10-28

The intestinal microbiota plays an important role in inflammatory bowel disease (IBD). The pathogenesis of IBD involves inappropriate ongoing activation of the mucosal immune system driven by abnormal intestinal microbiota in genetically predisposed individuals. However, there are still no definitive microbial pathogens linked to the onset of IBD. The composition and function of the intestinal microbiota and their metabolites are indeed disturbed in IBD patients. The special alterations of gut microbiota associated with IBD remain to be evaluated. The microbial interactions and host-microbe immune interactions are still not clarified. Limitations of present probiotic products in IBD are mainly due to modest clinical efficacy, few available strains and no standardized administration. Fecal microbiota transplantation (FMT) may restore intestinal microbial homeostasis, and preliminary data have shown the clinical efficacy of FMT on refractory IBD or IBD combined with Clostridium difficile infection. Additionally, synthetic microbiota transplantation with the defined composition of fecal microbiota is also a promising therapeutic approach for IBD. However, FMT-related barriers, including the mechanism of restoring gut microbiota, standardized donor screening, fecal material preparation and administration, and long-term safety should be resolved. The role of intestinal microbiota and FMT in IBD should be further investigated by metagenomic and metatranscriptomic analyses combined with germ-free/human flora-associated animals and chemostat gut models.

The fitness costs and trade-off shapes associated with the exclusion of nine antibiotics by OmpF porin channels.

PubMed

Phan, Katherine; Ferenci, Thomas

2017-06-01

The trade-off relationship between antibiotic exclusion and nutrient access across the Gram-negative outer membrane is determined by structural constraints in porin channels. The precise nutritional cost of exclusion is unknown for different antibiotics, as are the shapes of the nutrition-susceptibility trade-off. Using a library of 10 engineered isogenic Escherichia coli strains with structural modifications of OmpF porin expressed at a constant level, susceptibilities were measured for nine antibiotics and the nutritional fitness costs estimated by competitions in chemostats. Different antibiotics exhibited a remarkably varied range of geometries in the nutrition-susceptibility trade-off, including convex, concave and sigmoidal trade-off shapes. The trade-off patterns predict the possibility of adaptations in contributing to antibiotic resistance; exclusion of amoxicillin or trimethoprim in ompF mutants can occur with little loss of fitness whereas kanamycin and streptomycin exclusion has a high cost. Some individual OmpF changes even allow positive correlations (trade-ups), resulting in increased fitness and decreased susceptibility specifically to cephalexin or ciprofloxacin. The surprising plasticity of the nutrition-exclusion relationship means that there are no generalisable rules that apply to decreasing susceptibility for all antibiotics. The protein changes are exquisitely specific in determining nutritional fitness and adaptive outcomes in a structural constraint trade-off.

Involvement of Vacuolar Sequestration and Active Transport in Tolerance of Saccharomyces cerevisiae to Hop Iso-α-Acids▿ † ¶

PubMed Central

Hazelwood, Lucie A.; Walsh, Michael C.; Pronk, Jack T.; Daran, Jean-Marc

2010-01-01

The hop plant, Humulus lupulus L., has an exceptionally high content of secondary metabolites, the hop α-acids, which possess a range of beneficial properties, including antiseptic action. Studies performed on the mode of action of hop iso-α-acids have hitherto been restricted to lactic acid bacteria. The present study investigated molecular mechanisms of hop iso-α-acid resistance in the model eukaryote Saccharomyces cerevisiae. Growth inhibition occurred at concentrations of hop iso-α-acids that were an order of magnitude higher than those found with hop-tolerant prokaryotes. Chemostat-based transcriptome analysis and phenotype screening of the S. cerevisiae haploid gene deletion collection were used as complementary methods to screen for genes involved in hop iso-α-acid detoxification and tolerance. This screening and further analysis of deletion mutants confirmed that yeast tolerance to hop iso-α-acids involves three major processes, active proton pumping into the vacuole by the vacuolar-type ATPase to enable vacuolar sequestration of iso-α-acids and alteration of cell wall structure and, to a lesser extent, active export of iso-α-acids across the plasma membrane. Furthermore, iso-α-acids were shown to affect cellular metal homeostasis by acting as strong zinc and iron chelators. PMID:19915041

Standardized Assay Medium To Measure Lactococcus lactis Enzyme Activities while Mimicking Intracellular Conditions

PubMed Central

Goel, Anisha; Santos, Filipe; de Vos, Willem M.; Teusink, Bas

2012-01-01

Knowledge of how the activity of enzymes is affected under in vivo conditions is essential for analyzing their regulation and constructing models that yield an integrated understanding of cell behavior. Current kinetic parameters for Lactococcus lactis are scattered through different studies and performed under different assay conditions. Furthermore, assay conditions often diverge from conditions prevailing in the intracellular environment. To establish uniform assay conditions that resemble intracellular conditions, we analyzed the intracellular composition of anaerobic glucose-limited chemostat cultures of L. lactis subsp. cremoris MG 1363. Based on this, we designed a new assay medium for enzyme activity measurements of growing cells of L. lactis, mimicking as closely as practically possible its intracellular environment. Procedures were optimized to be carried out in 96-well plates, and the reproducibility and dynamic range were checked for all enzyme activity measurements. The effects of freezing and the carryover of ammonium sulfate from the addition of coupling enzymes were also established. Activities of all 10 glycolytic and 4 fermentative enzymes were measured. Remarkably, most in vivo-like activities were lower than previously published data. Yet, the ratios of Vmax over measured in vivo fluxes were above 1. With this work, we have developed and extensively validated standard protocols for enzyme activity measurements for L. lactis. PMID:22020503

Potential for mcl-PHA production from nonanoic and azelaic acids.

PubMed

Gillis, James; Ko, Kenton; Ramsay, Juliana A; Ramsay, Bruce A

2018-01-01

Greater than 65% of canola and high-oleic soy oil fatty acids is oleic acid, which is readily converted to nonanoic (NA) and azelaic (AzA) acids by ozonolysis. NA is an excellent substrate for medium-chain-length polyhydroxyalkanoate (mcl-PHA) production but AzA has few uses. Pseudomonas citronellolis DSM 50332 and Pseudomonas fluorescens ATCC 17400, both able to produce mcl-PHA from fatty acids and to grow on AzA as the sole source of carbon and energy, were assessed for the accumulation of mcl-PHA from AzA and NA. In N-limited shake flasks using NA, P. citronellolis produced 32% of its dry biomass as mcl-PHA containing 78% 3-hydroxynonanoate with 22% 3-hydroxyheptanoate. Pseudomonas fluorescens produced only 2% PHA. N-limited P. citronellolis on AzA produced 20% dry weight PHA containing 75% 3-hydroxydecanoate and 25% 3-hydroxyoctanoate, indicative of de novo synthesis. Although selective pressure, including β-oxidation inhibition, under well-controlled (chemostat) conditions was applied to P. citronellolis, no side-chain carboxyl groups were detected. It was concluded that one or more of FabG and PhaJ or the PHA synthase cannot catalyze reactions involving ω-carboxy substrates. However, a process based on oleic acid could be established if Pseudomonas putida was engineered to grow on AzA.

Metabolic Flux and Fitness

PubMed Central

Dykhuizen, Daniel E.; Dean, Antony M.; Hartl, Daniel L.

1987-01-01

Studies of Escherichia coli under competition for lactose in chemostat cultures have been used to determine the selective effects of variation in the level of the β-galactoside permease and the β-galactosidase enzyme. The results determine the adaptive topography of these gene products relative to growth in limiting lactose and enable predictions concerning the selective effects of genetic variants found in natural populations. In the terms of metabolic control theory, the β-galactosidase enzyme at wild-type-induced levels has a small control coefficient with respect to fitness (C = 0.018), and hence genetic variants resulting in minor changes in enzyme activity have disproportionately small effects on fitness. However, the apparent control coefficient of the β-galactoside permease at wild-type-induced levels is large (C = 0.551), and hence even minor changes in activity affect fitness. Therefore, we predict that genetic polymorphisms in the lacZ gene are subject to less effective selection in natural populations than are those in the lacY gene. The β-galactoside permease is also less efficient than might be expected, and possible forces resulting in selection for an intermediate optimum level of permease activity are considered. The selective forces that maintain the lactose operon in a regulated state in natural populations are also discussed. PMID:3104135

Characterization of the newly isolated ω-oxidizing yeast Candida sorbophila DS02 and its potential applications in long-chain dicarboxylic acid production.

PubMed

Lee, Heeseok; Sugiharto, Yohanes Eko Chandra; Lee, Seunghoon; Park, Gyuyeon; Han, Changpyo; Jang, Hyeran; Jeon, Wooyoung; Park, Heejoon; Ahn, Jungoh; Kang, Kyungbo; Lee, Hongwoen

2017-08-01

α, ω-Dicarboxylic acids (DCAs) are multipurpose chemicals widely used in polymers, perfumes, plasticizers, lubricants, and adhesives. The biotransformation of DCAs from alkanes and fatty acids by microorganisms has attracted recent interest, since synthesis via chemical oxidation causes problems in terms of the environment and safety. We isolated an ω-oxidizing yeast from a wastewater disposal facility of a petrochemical factory by chemostat enrichment culture. The haploid strain identified as Candida sorbophila DS02 grew on glucose and dodecane, exhibiting greater cell shrinkage on the latter. In flask cultures with mixed alkanes (C10-16) and fatty acid methyl esters (C10-16), DS02 used mixed alkanes simultaneously unlike Candida tropicalis and Yarrowia lipolytica and showed high substrate resistance. In flask cultures with acrylic acid-a known inhibitor of β-oxidation-DS02 produced 0.28 g/l dodecanedioic acid (DDDA) from dodecane, similar to wild-type C. tropicalis ATCC 20336. In fed-batch fermentation, DS02 produced 9.87 g/l DDDA, which was 5.7-fold higher than wild-type C. tropicalis. These results suggest that C. sorbophila strain DS02 has potential applications for the large-scale production of DCA.

In situ gene expression profiling of the thermoacidophilic alga Cyanidioschyzon in relation to visible and ultraviolet irradiance.

PubMed

Skorupa, Dana J; Castenholz, Richard W; Mazurie, Aurélien; Carey, Charles; Rosenzweig, Frank; McDermott, Timothy R

2014-06-01

Ultraviolet and high-intensity visible radiation generate reactive intermediates that damage phototrophic microorganisms. In Yellowstone National Park, the thermoacidophilic alga Cyanidioschyzon exhibits an annual seasonal biomass fluctuation referred to as 'mat decline', where algal viability decreases as ultraviolet and visible irradiances increase during summer. We examined the role irradiance might play in mat decline using irradiance filters that uncouple ultraviolet and visible effects along with custom microarrays to study gene expression in situ. Of the 6507 genes, 88% showed no response to ultraviolet or visible, implying that at the biomolecular level, these algae inhabit a chemostat-like environment and is consistent with the near constant aqueous chemistry measured. The remaining genes exhibited expression changes linked to ultraviolet exposure, to increased visible radiation, or to the apparent combined effects of ultraviolet and visible. Expression of DNA repetitive elements was synchronized, being repressed by visible but also influenced by ultraviolet. At highest irradiance levels, these algae reduced transcription of genes encoding functions involved with DNA replication, photosynthesis and cell cycle progression but exhibited an uptick in activities related to repairing DNA damage. This corroborates known physiological responses to ultraviolet and visible radiation, and leads us to provisionally conclude that mat decline is linked to photoinhibition. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

PubMed

Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

2014-01-01

A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

Proteomic Analysis of Carbon Concentrating Chemolithotrophic Bacteria Serratia sp. for Sequestration of Carbon Dioxide

PubMed Central

Bharti, Randhir K.; Srivastava, Shaili; Thakur, Indu Shekhar

2014-01-01

A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials. PMID:24619032

Anaerobic Biodegradation of Soybean Biodiesel and Diesel ...

EPA Pesticide Factsheets

Biotransformation of soybean biodiesel and the inhibitory effect of petrodiesel were studied under methanogenic conditions. Biodiesel removal efficiency of more than 95% was achieved in a chemostat with influent biodiesel concentrations up to 2.45 g/L. The kinetics of anaerobic biodegradation of soybean biodiesel B100 (biodiesel only) with different petrodiesel loads were studied using biomass pre-acclimated to B100 and B80 (80% biodiesel and 20 petrodiesel). The results indicated that the biodiesel fraction of the blend could be effectively biodegraded, whereas petrodiesel was not biodegraded at all under methanogenic conditions. The presence of petrodiesel in blends with biodiesel had a greater inhibitory effect on the rate of biodegradation than the biodegradation efficiency (defined as the efficiency of methane production). Both the biodegradation rate coefficient and the methane production efficiency increased almost linearly with the increasing fraction of biodiesel. With the increasing fraction of petrodiesel, the biodegradation rate and efficiency were correlated with the concentration of soluble FAMEs in the water. The objective of this study was to investigate the anaerobic biodegradation of soybean biodiesel blends under methanogenic conditions. Biological methane potential (BMP) tests were conducted in serum bottles to determine the anaerobic biodegradation kinetics of biodiesel in the absence and presence of different concentrations of petrod

Potential and Prospects of Continuous Polyhydroxyalkanoate (PHA) Production

PubMed Central

Koller, Martin; Braunegg, Gerhart

2015-01-01

Together with other so-called “bio-plastics”, Polyhydroxyalkanoates (PHAs) are expected to soon replace established polymers on the plastic market. As a prerequisite, optimized process design is needed to make PHAs attractive in terms of costs and quality. Nowadays, large-scale PHA production relies on discontinuous fed-batch cultivation in huge bioreactors. Such processes presuppose numerous shortcomings such as nonproductive time for reactor revamping, irregular product quality, limited possibility for supply of certain carbon substrates, and, most of all, insufficient productivity. Therefore, single- and multistage continuous PHA biosynthesis is increasingly investigated for production of different types of microbial PHAs; this goes for rather crystalline, thermoplastic PHA homopolyesters as well as for highly flexible PHA copolyesters, and even blocky-structured PHAs consisting of alternating soft and hard segments. Apart from enhanced productivity and constant product quality, chemostat processes can be used to elucidate kinetics of cell growth and PHA formation under constant process conditions. Furthermore, continuous enrichment processes constitute a tool to isolate novel powerful PHA-producing microbial strains adapted to special environmental conditions. The article discusses challenges, potential and case studies for continuous PHA production, and shows up new strategies to further enhance such processes economically by developing unsterile open continuous processes combined with the application of inexpensive carbon feedstocks. PMID:28955015

Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress.

PubMed

Muller, Jocelyn Fraga; Stevens, Ann M; Craig, Johanna; Love, Nancy G

2007-07-01

Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole-genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium, Pseudomonas aeruginosa, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole-cell acetate uptake rates (WAURs) and cell viability and for gene expression changes by Affymetrix GeneChip technology and real-time reverse transcriptase PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multidrug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant.

Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae.

PubMed

Elbing, Karin; Larsson, Christer; Bill, Roslyn M; Albers, Eva; Snoep, Jacky L; Boles, Eckhard; Hohmann, Stefan; Gustafsson, Lena

2004-09-01

The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which has distinct glucose transport characteristics. The strains display a range of decreasing glycolytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type S. cerevisiae does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycolysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in S. cerevisiae and will provide new tools for the control of industrial fermentations.

Role of Hexose Transport in Control of Glycolytic Flux in Saccharomyces cerevisiae

PubMed Central

Elbing, Karin; Larsson, Christer; Bill, Roslyn M.; Albers, Eva; Snoep, Jacky L.; Boles, Eckhard; Hohmann, Stefan; Gustafsson, Lena

2004-01-01

The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which has distinct glucose transport characteristics. The strains display a range of decreasing glycolytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type S. cerevisiae does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycolysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in S. cerevisiae and will provide new tools for the control of industrial fermentations. PMID:15345416

A methodology for a quantitative interpretation of DGGE with the help of mathematical modelling: application in biohydrogen production.

PubMed

Tapia, Estela; Donoso-Bravo, Andres; Cabrol, Léa; Alves, Madalena; Pereira, Alcina; Rapaport, Alain; Ruiz-Filippi, Gonzalo

2014-01-01

Molecular biology techniques provide valuable insights in the investigation of microbial dynamics and evolution. Denaturing gradient gel electrophoresis (DGGE) analysis is one of the most popular methods which have been used in bioprocess assessment. Most of the anaerobic digestion models consider several microbial populations as state variables. However, the difficulty of measuring individual species concentrations may cause inaccurate model predictions. The integration of microbial data and ecosystem modelling is currently a challenging issue for improved system control. A novel procedure that combines common experimental measurements, DGGE, and image analysis is presented in this study in order to provide a preliminary estimation of the actual concentration of the dominant bacterial ribotypes in a bioreactor, for further use as a variable in mathematical modelling of the bioprocess. This approach was applied during the start-up of a continuous anaerobic bioreactor for hydrogen production. The experimental concentration data were used for determining the kinetic parameters of each species, by using a multi-species chemostat-model. The model was able to reproduce the global trend of substrate and biomass concentrations during the reactor start-up, and predicted in an acceptable way the evolution of each ribotype concentration, depicting properly specific ribotype selection and extinction.

Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose.

PubMed

Panagiotou, Gianni; Christakopoulos, Paul; Grotkjaer, Thomas; Olsson, Lisbeth

2006-09-01

Dissimilatory nitrate reduction metabolism, of the natural xylose-fermenting fungus Fusarium oxysporum, was used as a strategy to achieve anaerobic growth and ethanol production from xylose. Beneficial alterations of the redox fluxes and thereby of the xylose metabolism were obtained by taking advantage of the regeneration of the cofactor NAD(+) during the denitrification process. In batch cultivations, nitrate sustained growth under anaerobic conditions (1.21 g L(-1) biomass) and simultaneously a maximum yield of 0.55 moles of ethanol per mole of xylose was achieved, whereas substitution of nitrate with ammonium limited the growth significantly (0.15 g L(-1) biomass). Using nitrate, the maximum acetate yield was 0.21 moles per mole of xylose and no xylitol excretion was observed. Furthermore, the network structure in the central carbon metabolism of F. oxysporum was characterized in steady state. F. oxysporum grew anaerobically on [1-(13)C] labelled glucose and unlabelled xylose in chemostat cultivation with nitrate as nitrogen source. The use of labelled substrate allowed the precise determination of the glucose and xylose contribution to the carbon fluxes in the central metabolism of this poorly described microorganism. It was demonstrated that dissimilatory nitrate reduction allows F. oxysporum to exhibit typical respiratory metabolic behaviour with a highly active TCA cycle and a large demand for NADPH.

Intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease

PubMed Central

Wang, Zi-Kai; Yang, Yun-Sheng; Chen, Ye; Yuan, Jing; Sun, Gang; Peng, Li-Hua

2014-01-01

The intestinal microbiota plays an important role in inflammatory bowel disease (IBD). The pathogenesis of IBD involves inappropriate ongoing activation of the mucosal immune system driven by abnormal intestinal microbiota in genetically predisposed individuals. However, there are still no definitive microbial pathogens linked to the onset of IBD. The composition and function of the intestinal microbiota and their metabolites are indeed disturbed in IBD patients. The special alterations of gut microbiota associated with IBD remain to be evaluated. The microbial interactions and host-microbe immune interactions are still not clarified. Limitations of present probiotic products in IBD are mainly due to modest clinical efficacy, few available strains and no standardized administration. Fecal microbiota transplantation (FMT) may restore intestinal microbial homeostasis, and preliminary data have shown the clinical efficacy of FMT on refractory IBD or IBD combined with Clostridium difficile infection. Additionally, synthetic microbiota transplantation with the defined composition of fecal microbiota is also a promising therapeutic approach for IBD. However, FMT-related barriers, including the mechanism of restoring gut microbiota, standardized donor screening, fecal material preparation and administration, and long-term safety should be resolved. The role of intestinal microbiota and FMT in IBD should be further investigated by metagenomic and metatranscriptomic analyses combined with germ-free/human flora-associated animals and chemostat gut models. PMID:25356041

Kinetics of nitrification in a fixed biofilm reactor using dewatered sludge-fly ash composite ceramic particle as a supporting medium.

PubMed

Lee, Mong-Chuan; Lin, Yen-Hui; Yu, Huang-Wei

2014-11-01

A mathematical model system was derived to describe the kinetics of ammonium nitrification in a fixed biofilm reactor using dewatered sludge-fly ash composite ceramic particle as a supporting medium. The model incorporates diffusive mass transport and Monod kinetics. The model was solved using a combination of the orthogonal collocation method and Gear's method. A batch test was conducted to observe the nitrification of ammonium-nitrogen ([Formula: see text]-N) and the growth of nitrifying biomass. The compositions of nitrifying bacterial community in the batch kinetic test were analyzed using PCR-DGGE method. The experimental results show that the most staining intensity abundance of bands occurred on day 2.75 with the highest biomass concentration of 46.5 mg/L. Chemostat kinetic tests were performed independently to evaluate the biokinetic parameters used in the model prediction. In the column test, the removal efficiency of [Formula: see text]-N was approximately 96 % while the concentration of suspended nitrifying biomass was approximately 16 mg VSS/L and model-predicted biofilm thickness reached up to 0.21 cm in the steady state. The profiles of denaturing gradient gel electrophoresis (DGGE) of different microbial communities demonstrated that indigenous nitrifying bacteria (Nitrospira and Nitrobacter) existed and were the dominant species in the fixed biofilm process.

Quantitative metabolomics of the thermophilic methylotroph Bacillus methanolicus.

PubMed

Carnicer, Marc; Vieira, Gilles; Brautaset, Trygve; Portais, Jean-Charles; Heux, Stephanie

2016-06-01

The gram-positive bacterium Bacillus methanolicus MGA3 is a promising candidate for methanol-based biotechnologies. Accurate determination of intracellular metabolites is crucial for engineering this bacteria into an efficient microbial cell factory. Due to the diversity of chemical and cell properties, an experimental protocol validated on B. methanolicus is needed. Here a systematic evaluation of different techniques for establishing a reliable basis for metabolome investigations is presented. Metabolome analysis was focused on metabolites closely linked with B. methanolicus central methanol metabolism. As an alternative to cold solvent based procedures, a solvent-free quenching strategy using stainless steel beads cooled to -20 °C was assessed. The precision, the consistency of the measurements, and the extent of metabolite leakage from quenched cells were evaluated in procedures with and without cell separation. The most accurate and reliable performance was provided by the method without cell separation, as significant metabolite leakage occurred in the procedures based on fast filtration. As a biological test case, the best protocol was used to assess the metabolome of B. methanolicus grown in chemostat on methanol at two different growth rates and its validity was demonstrated. The presented protocol is a first and helpful step towards developing reliable metabolomics data for thermophilic methylotroph B. methanolicus. This will definitely help for designing an efficient methylotrophic cell factory.

Sensitivity of chemical weathering and dissolved carbon dynamics to hydrological conditions in a typical karst river

PubMed Central

Zhong, Jun; Li, Si-liang; Tao, Faxiang; Yue, Fujun; Liu, Cong-Qiang

2017-01-01

To better understand the mechanisms that hydrological conditions control chemical weathering and carbon dynamics in the large rivers, we investigated hydrochemistry and carbon isotopic compositions of dissolved inorganic carbon (DIC) based on high-frequency sampling in the Wujiang River draining the carbonate area in southwestern China. Concentrations of major dissolved solute do not strictly follow the dilution process with increasing discharge, and biogeochemical processes lead to variability in the concentration-discharge relationships. Temporal variations of dissolved solutes are closely related to weathering characteristics and hydrological conditions in the rainy seasons. The concentrations of dissolved carbon and the carbon isotopic compositions vary with discharge changes, suggesting that hydrological conditions and biogeochemical processes control dissolved carbon dynamics. Biological CO2 discharge and intense carbonate weathering by soil CO2 should be responsible for the carbon variability under various hydrological conditions during the high-flow season. The concentration of DICbio (DIC from biological sources) derived from a mixing model increases with increasing discharge, indicating that DICbio influx is the main driver of the chemostatic behaviors of riverine DIC in this typical karst river. The study highlights the sensitivity of chemical weathering and carbon dynamics to hydrological conditions in the riverine system. PMID:28220859

Levels of cyclic-2,3-diphosphoglycerate in Methanobacterium thermoautotrophicum during phosphate limitation.

PubMed Central

Seely, R J; Fahrney, D E

1984-01-01

Batch-grown Methanobacterium thermoautotrophicum cells grew nonexponentially in the absence of exogenous Pi until intracellular cyclic-2,3-diphosphoglycerate (cyclic DPG) had fallen below 2 mumol/g (dry weight), the limit of detection. Growth resumed immediately upon transfer to medium containing Pi Cyclic DPG levels were also below detection in Pi-limited chemostat cultures operating at a dilution rate of 0.173 h-1 (4-h doubling time), with reservoir Pi concentrations below 200 microM. At this dilution rate, the Pi concentration in the culture was 4 microM. An H2-limited steady state was achieved with 400 microM Pi in the inflowing medium (67 microM in the culture). The cyclic DPG content of these cells was 72 to 74 mumol/g, about one-third the amount in batch-grown cells. The specific growth rate accelerated immediately to 0.36 h-1 (1.9-h doubling time) under washout conditions at high dilution rate. The cellular content of cyclic DPG declined over a 2-h period, and then increased rapidly as the Pi level in the medium approached 200 microM. Expansion of the cyclic DPG pool coincided with a marked increase in Pi assimilation. These results indicated that M. thermoautotrophicum accumulated cyclic DPG only when Pi and H2 were readily available. PMID:6480564

Levels of cyclic-2,3-diphosphoglycerate in Methanobacterium thermoautotrophicum during phosphate limitation.

PubMed

Seely, R J; Fahrney, D E

1984-10-01

Batch-grown Methanobacterium thermoautotrophicum cells grew nonexponentially in the absence of exogenous Pi until intracellular cyclic-2,3-diphosphoglycerate (cyclic DPG) had fallen below 2 mumol/g (dry weight), the limit of detection. Growth resumed immediately upon transfer to medium containing Pi Cyclic DPG levels were also below detection in Pi-limited chemostat cultures operating at a dilution rate of 0.173 h-1 (4-h doubling time), with reservoir Pi concentrations below 200 microM. At this dilution rate, the Pi concentration in the culture was 4 microM. An H2-limited steady state was achieved with 400 microM Pi in the inflowing medium (67 microM in the culture). The cyclic DPG content of these cells was 72 to 74 mumol/g, about one-third the amount in batch-grown cells. The specific growth rate accelerated immediately to 0.36 h-1 (1.9-h doubling time) under washout conditions at high dilution rate. The cellular content of cyclic DPG declined over a 2-h period, and then increased rapidly as the Pi level in the medium approached 200 microM. Expansion of the cyclic DPG pool coincided with a marked increase in Pi assimilation. These results indicated that M. thermoautotrophicum accumulated cyclic DPG only when Pi and H2 were readily available.

Ammonia assimilation and synthesis of alanine, aspartate, and glutamate in Methanosarcina barkeri and Methanobacterium thermoautotrophicum.

PubMed Central

Kenealy, W R; Thompson, T E; Schubert, K R; Zeikus, J G

1982-01-01

The mechanism of ammonia assimilation in Methanosarcina barkeri and Methanobacterium thermoautotrophicum was documented by analysis of enzyme activities, 13NH3 incorporation studies, and comparison of growth and enzyme activity levels in continuous culture. Glutamate accounted for 65 and 52% of the total amino acids in the soluble pools of M. barkeri and M. thermoautotrophicum. Both organisms contained significant activities of glutamine synthetase, glutamate synthase, glutamate oxaloacetate transaminase, and glutamate pyruvate transaminase. Hydrogen-reduced deazaflavin-factor 420 or flavin mononucleotide but not NAD, NADP, or ferredoxin was used as the electron donor for glutamate synthase in M. barkeri. Glutamate dehydrogenase activity was not detected in either organism, but alanine dehydrogenase activity was present in M. thermoautotrophicum. The in vivo activity of the glutamine synthetase was verified in M. thermoautotrophicum by analysis of 13NH3 incorporation into glutamine, glutamate, and alanine. Alanine dehydrogenase and glutamine synthetase activity varied in response to [NH4+] when M. thermoautotrophicum was cultured in a chemostat with cysteine as the sulfur source. Alanine dehydrogenase activity and growth yield (grams of cells/mole of methane) were highest when the organism was cultured with excess ammonia, whereas growth yield was lower and glutamine synthetase was maximal when ammonia was limiting. PMID:6122678

Enzymic activities of cadmium- and zinc-tolerant strains of Klebsiella (Aerobacter) aerogenes growing in glucose-limited chemostats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pickett, A.W.; Carter, I.S.; Dean, A.C.R.

The activities of phosphatases and some enzymes of glucose metabolism were determined in K. aerogenes NCIB 418 and in two strains derived from it, resistant to 50 ..mu..g Cd/sup 2 +/ ml/sup -1/ and 16..mu..g Zn/sup 2 +/ ml/sup -1/ respectively, during growth at D = 0.38 h/sup -1/ in medium containing ..beta..-glycerophosphate as sole phosphorus source and supplemented with Cd/sup 2 +/ and Zn/sup 2 +/, as appropriate for the resistant strains. The pH-activity profiles of the phosphatases differed from strain to strain but all showed maximum activity at an acid pH and this activity was very much lowermore » in the Zn/sup 2 +/-resistant strain than in the control and even lower in the Cd/sup 2 +/-resistant strain. Resistance to either metal was associated with decreased glucose-6-phosphate dehydrogenase activity and increased phosphoglucose isomerase activity, suggesting an increased flow of carbon through the Embden-Meyerhof pathway relative to the pentose phosphate pathway, but the efficiency of the conversion of glucose into biomass was largely unaffected. Glucose phosphoenolpyruvate phosphotransferase activity was also lower in the resistant strains. 25 references, 1 figure, 1 table.« less

Phosphorus Export Model Development in a Terminal Lake Basin using Concentration-Streamflow Relationship

NASA Astrophysics Data System (ADS)

Jeannotte, T.; Mahmood, T. H.; Matheney, R.; Hou, X.

2017-12-01

Nutrient export to streams and lakes by anthropogenic activities can lead to eutrophication and degradation of surface water quality. In Devils Lake, ND, the only terminal lake in the Northern Great Plains, the algae boom is of great concern due to the recent increase in streamflow and consequent rise in phosphorus (P) export from prairie agricultural fields. However, to date, very few studies explored the concentration (c) -streamflow (q) relationship in the headwater catchments of the Devils Lake basin. A robust watershed-scale quantitative framework would aid understanding of the c-q relationship, simulating P concentration and load. In this study, we utilize c-q relationships to develop a simple model to estimate phosphorus concentration and export from two headwater catchments of different size (Mauvais Coulee: 1032 km2 and Trib 3: 160 km2) draining to Devils Lake. Our goal is to link the phosphorus export model with a physically based hydrologic model to identify major drivers of phosphorus export. USGS provided the streamflow measurements, and we collected water samples (filtered and unfiltered) three times daily during the spring snowmelt season (March 31, 2017- April 12, 2017) at the outlets of both headwater catchments. Our results indicate that most P is dissolved and very little is particulate, suggesting little export of fine-grained sediment from agricultural fields. Our preliminary analyses in the Mauvais Coulee catchment show a chemostatic c-q relationship in the rising limb of the hydrograph, while the recession limb shows a linear and positive c-q relationship. The poor correlation in the rising limb of the hydrograph suggests intense flushing of P by spring snowmelt runoff. Flushing then continues in the recession limb of the hydrograph, but at a more constant rate. The estimated total P load for the Mauvais Coulee basin is 193 kg/km2, consistent with other catchments of similar size across the Red River of the North basin to the east. We expect our P measurements at Trib 3 basin, a considerably smaller basin compared to Mauvais Coulee, provide an opportunity to investigate the impacts of watershed scales on nutrient exports and c-q relationship. Finally, our study will lay a strong foundation for future nutrient modeling studies in the Devils Lake basin.

In vivo analysis of NH4+ transport and central N-metabolism of Saccharomyces cerevisiae under aerobic N-limited conditions.

PubMed

Cueto-Rojas, H F; Maleki Seifar, R; Ten Pierick, A; van Helmond, W; Pieterse M, M; Heijnen, J J; Wahl, S A

2016-09-16

Ammonium is the most common N-source for yeast fermentations. Although, its transport and assimilation mechanisms are well documented, there have been only few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N-sources (ammonium, urea and glutamate) at the same growth rate (0.05 h -1 ). The experimental results suggest that, at this growth rate, a similar concentration of intracellular ammonium, about 3.6 mmol NH 4 + /L IC , is required to supply the reactions in the central N-metabolism independent of the N-source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH 3 leakage to the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between reactions Gdh1 and Gdh2. Finally, using shotgun proteomics with labeled reference-relative protein expression, differences between the various environmental conditions were identified and correlated with previously identified N-compound sensing mechanisms. In our work, we study central N-metabolism using quantitative approaches. First, intracellular ammonium was measured under different N-sources. The results suggest that Saccharomyces cerevisiae cells keep a constant NH 4 + concentration (around 3 mmol NH 4 + /L IC ), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force.Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally distributed, indicating a high degree of compartmentalization in the vacuole. Additionally, metabolomic analysis results were used to calculate the thermodynamic driving forces in the central N-metabolism reactions, revealing that the main reactions in the central N-metabolism are far from equilibrium. Using proteomics approaches, we were able to identify major changes, not only in N-metabolism but also C-metabolism and regulation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth

PubMed Central

Maleki Seifar, R.; ten Pierick, A.; van Helmond, W.; Pieterse, M. M.; Heijnen, J. J.

2016-01-01

ABSTRACT Ammonium is the most common N source for yeast fermentations. Although its transport and assimilation mechanisms are well documented, there have been only a few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method, we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N sources (ammonium, urea, and glutamate) at the same growth rate (0.05 h−1). The experimental results suggest that, at this growth rate, a similar concentration of intracellular (IC) ammonium, about 3.6 mmol NH4+/literIC, is required to supply the reactions in the central N metabolism, independent of the N source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH3 leakage into the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between Gdh1 and Gdh2 reactions. Finally, using shotgun proteomics with protein expression determined relative to a labeled reference, differences between the various environmental conditions were identified and correlated with previously identified N compound-sensing mechanisms. IMPORTANCE In our work, we studied central N metabolism using quantitative approaches. First, intracellular ammonium was measured under different N sources. The results suggest that Saccharomyces cerevisiae cells maintain a constant NH4+ concentration (around 3 mmol NH4+/literIC), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force. Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally distributed, indicating a high degree of compartmentalization in the vacuole. Additionally, metabolomic analysis results were used to calculate the thermodynamic driving forces in the central N metabolism reactions, revealing that the main reactions in the central N metabolism are far from equilibrium. Using proteomics approaches, we were able to identify major changes, not only in N metabolism, but also in C metabolism and regulation. PMID:27637876

Benthic long-term Observatories based on Lander Technology

NASA Astrophysics Data System (ADS)

Linke, P.; Pfannkuche, O.; Sommer, S.; Gubsch, S.; Gust, G.

2003-04-01

Landers are autonomous carrier systems for a wide range of scientific applications. The GEOMAR Lander System is based on a tripod-shaped platform for various scientific payloads to monitor, measure and experiment at the deep sea floor. These landers can be deployed using hybrid fibre optical or coaxial cables with a special launching device or in the conventional free falling mode. The launcher enables accurate positioning on meter scale, soft deployment and rapid disconnection of lander and launcher by an electric release. The bi-directional video and data telemetry provides on line video transmission, power supply and surface control of various relay functions. Within the collaborative project LOTUS novel long-term observatories have been developed and integrated into the GEOMAR Lander System. An overview of the recent developments is presented. Two new observatories are presented in detail to study the temporal variability of physico-chemical and biogeochemical mechanisms, flux- and turnover rates related to the decomposition and formation of near surface gas hydrates embedded in their original sedimentary matrix. With the Biogeochemical Observatory, BIGO, the temporal variability of the biologically facilitated methane turnover in the sediment and fluxes across the sediment water interface is studied in two mesocosms. Inside the mesocosms the oxygen content can be maintained by a chemostat. The in situ flow regime is measured outside the mesocosms and is reproduced within the chamber with an intelligent stirring system. This approach represents a major step in the development of benthic chambers from stationary to dynamic systems. The Fluid-Flux Observatory (FLUFO) measures the different types of fluid fluxes at the benthic boundary layer of sediments overlying near surface gas hydrates and monitors relevant environmental parameters as temperature, pressure and near bottom currents. FLUFO consists of two chamber units. Both units separate the gas phase from the aqueous phase and measure their individual contribution to the total fluid flux. Whereas the first (reference) chamber measures the aqueous flux without obtaining information about their direction, the second (FLUFO) chamber measures the aqueous flux including the direction discriminating between outward flow, stagnation and inward flow.

Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures

PubMed Central

2012-01-01

Background The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as sole carbon source have been shown to improve product productivities and alleviate metabolic burden derived from protein production. Nevertheless, systematic quantitative studies on the relationships between the central metabolism and recombinant protein production in P. pastoris are still rather limited, particularly when growing this yeast on mixed carbon sources, thus hampering future metabolic network engineering strategies for improved protein production. Results The metabolic flux distribution in the central metabolism of P. pastoris growing on a mixed feed of glucose and methanol was analyzed by Metabolic Flux Analysis (MFA) using 13C-NMR-derived constraints. For this purpose, we defined new flux ratios for methanol assimilation pathways in P. pastoris cells growing on glucose:methanol mixtures. By using this experimental approach, the metabolic burden caused by the overexpression and secretion of a Rhizopus oryzae lipase (Rol) in P. pastoris was further analyzed. This protein has been previously shown to trigger the unfolded protein response in P. pastoris. A series of 13C-tracer experiments were performed on aerobic chemostat cultivations with a control and two different Rol producing strains growing at a dilution rate of 0.09 h−1 using a glucose:methanol 80:20 (w/w) mix as carbon source. The MFA performed in this study reveals a significant redistristribution of carbon fluxes in the central carbon metabolism when comparing the two recombinant strains vs the control strain, reflected in increased glycolytic, TCA cycle and NADH regeneration fluxes, as well as higher methanol dissimilation rates. Conclusions Overall, a further 13C-based MFA development to characterise the central metabolism of methylotrophic yeasts when growing on mixed methanol:multicarbon sources has been implemented, thus providing a new tool for the investigation of the relationships between central metabolism and protein production. Specifically, the study points at a limited but significant impact of the conformational stress associated to secretion of recombinant proteins on the central metabolism, occurring even at modest production levels. PMID:22569166

Effect of salinity on 2H/1H fractionation in lipids from continuous cultures of the coccolithophorid Emiliania huxleyi

NASA Astrophysics Data System (ADS)

Sachs, Julian P.; Maloney, Ashley E.; Gregersen, Josh; Paschall, Christopher

2016-09-01

Salinity and temperature dictate the buoyancy of seawater, and by extension, ocean circulation and heat transport. Yet there remain few widely applicable proxies for salinity with the precision necessary to infer all but the largest hydrographic variations in the past. In the last decade the hydrogen isotope composition (2H/1H or δ2H) of microalgal lipids has been shown to increase systematically with salinity, providing a foundation for its use as a paleosalinity proxy. Culture and field studies have indicated a wide range of sensitivities for this response, ranging from about 0.6-3.3‰ ppt-1 depending on the lipid, location and/or culturing conditions. Lacking in these studies has been the controlled conditions necessary to isolate the response to salinity while keeping all other growth parameters constant. Here we show that the hydrogen isotope composition of lipids in the marine coccolithophorid Emiliania huxleyi grown in chemostats increased by 1.6 ± 0.3‰ ppt-1 (p < 0.05) in eight individual alkenones and by 2.0 ± 0.1‰ ppt-1 (p < 0.05) in three individual fatty acids over the salinity range 20-42 ppt. Hydrogen isotope ratios of phytol and the sterol 24-methyl-cholest-5,22-dien-3β-ol (brassicasterol) also increased with salinity but correlations were weaker than for the acetogenic lipids. For eight individual alkenones, linear regression analyses of the fractionation factors on salinity yielded slopes of 1.2-2.2‰ ppt-1. This sensitivity of δ2Halkenone to salinity is 45-71% of that previously reported for E. huxleyi, which can be attributed to the fact that previous experiments were performed with batch cultures in which growth rates and other parameters differed between salinity treatments. The underlying cause of this response to salinity remains unknown, but may result from changes in (1) the proportion of lipid hydrogen derived from NADPH versus water, (2) the proportion of lipid hydrogen derived from NADPH from Photosystem I versus the oxidative pentose phosphate pathway (and other metabolic sources), or (3) the δ2H value of intracellular water.

The final results of the Mi-Beta Cryogenic Experiment towards the CUORICINO Experiment

NASA Astrophysics Data System (ADS)

Pirro, S.; Arnaboldi, C.; Brofferio, C.; Bucci, C.; Capelli, S.; Cremonesi, O.; Fiorini, E.; Giuliani, A.; McDonald, R. J.; Nucciotti, A.; Pavan, M.; Pedretti, M.; Pessina, G.; Pobes, C.; Previtali, E.; Sisti, M.; Vanzini, M.; Zanotti, L.

2002-02-01

We present the final results on neutrinoless Double Beta Decay (DBD) of 130Te obtained with an array of 20 cryogenic detectors. The Mi-Beta Experiment is operating since 3 years and was upgraded in March 2001. The background in the DBD energy region was reduced thanks to a new Roman lead shield framed inside the dilution unit and a neutron shield mounted outside the cryostat. We also improved the energy threshold using a cold electronic stage inside the cryostat. The new set-up represents also a good test for the CUORICINO Experiment. CUORICINO will start by the beginning of 2002 and will consist of 56 Tellurium Oxide Crystal with an overall bolometric mass of 42 kg. .

Preliminary design polymeric materials experiment. [for space shuttles and Spacelab missions

NASA Technical Reports Server (NTRS)

Mattingly, S. G.; Rude, E. T.; Marshner, R. L.

1975-01-01

A typical Advanced Technology Laboratory mission flight plan was developed and used as a guideline for the identification of a number of experiment considerations. The experiment logistics beginning with sample preparation and ending with sample analysis are then overlaid on the mission in order to have a complete picture of the design requirements. The results of this preliminary design study fall into two categories. First specific preliminary designs of experiment hardware which is adaptable to a variety of mission requirements. Second, identification of those mission considerations which affect hardware design and will require further definition prior to final design. Finally, a program plan is presented which will provide the necessary experiment hardware in a realistic time period to match the planned shuttle flights. A bibliography of all material reviewed and consulted but not specifically referenced is provided.

The Interrelationship between Student Learning Experience and Study Behaviour

ERIC Educational Resources Information Center

Ning, Hoi Kwan; Downing, Kevin

2011-01-01

This study examined the interrelationship between student learning experiences and study behaviour in explaining academic achievement. The participants were 541 final year students from a university in Hong Kong. Students' learning experiences and study behaviour were measured using the Course Experience Questionnaire and the Learning and Study…

10 CFR 50.59 - Changes, tests, and experiments.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Changes, tests, and experiments. 50.59 Section 50.59..., Limitations, and Conditions of Licenses and Construction Permits § 50.59 Changes, tests, and experiments. (a... operator actions and response times). (6) Tests or experiments not described in the final safety analysis...

10 CFR 72.48 - Changes, tests, and experiments.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 2 2012-01-01 2012-01-01 false Changes, tests, and experiments. 72.48 Section 72.48... Issuance and Conditions of License § 72.48 Changes, tests, and experiments. (a) Definitions for the... times). (7) Tests or experiments not described in the Final Safety Analysis Report (as updated) means...

10 CFR 50.59 - Changes, tests, and experiments.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Changes, tests, and experiments. 50.59 Section 50.59..., Limitations, and Conditions of Licenses and Construction Permits § 50.59 Changes, tests, and experiments. (a... operator actions and response times). (6) Tests or experiments not described in the final safety analysis...

10 CFR 72.48 - Changes, tests, and experiments.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false Changes, tests, and experiments. 72.48 Section 72.48... Issuance and Conditions of License § 72.48 Changes, tests, and experiments. (a) Definitions for the... times). (7) Tests or experiments not described in the Final Safety Analysis Report (as updated) means...

10 CFR 50.59 - Changes, tests, and experiments.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Changes, tests, and experiments. 50.59 Section 50.59..., Limitations, and Conditions of Licenses and Construction Permits § 50.59 Changes, tests, and experiments. (a... operator actions and response times). (6) Tests or experiments not described in the final safety analysis...

10 CFR 72.48 - Changes, tests, and experiments.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false Changes, tests, and experiments. 72.48 Section 72.48... Issuance and Conditions of License § 72.48 Changes, tests, and experiments. (a) Definitions for the... times). (7) Tests or experiments not described in the Final Safety Analysis Report (as updated) means...

The Influence of Growth Rate on 2H/1H Fractionation in Continuous Cultures of the Coccolithophorid Emiliania huxleyi and the Diatom Thalassiosira pseudonana

PubMed Central

Sachs, Julian P.; Kawka, Orest E.

2015-01-01

The hydrogen isotope (2H/1H) ratio of lipids from phytoplankton is a powerful new tool for reconstructing hydroclimate variations in the geologic past from marine and lacustrine sediments. Water 2H/1H changes are reflected in lipid 2H/1H changes with R2 > 0.99, and salinity variations have been shown to cause about a 1‰ change in lipid δ2H values per unit (ppt) change in salinity. Less understood are the effects of growth rate, nutrient limitation and light on 2H/1H fractionation in phytoplankton. Here we present the first published study of growth rate effects on 2H/1H fractionation in the lipids of coccolithophorids grown in continuous cultures. Emiliania huxleyi was cultivated in steady state at four growth rates and the δ2H value of individual alkenones (C37:2, C37:3, C38:2, C38:3), fatty acids (C14:0, C16:0, C18:0), and 24-methyl cholest-5,22-dien-3β-ol (brassicasterol) were measured. 2H/1H fractionation increased in all lipids as growth rate increased by 24‰ to 79‰ (div d-1)-1. We attribute this response to a proportional increase in the fraction of NADPH from Photosystem I (PS1) of photosynthesis relative to NADPH from the cytosolic oxidative pentose phosphate (OPP) pathway in the synthesis of lipids as growth rate increases. A 3-endmember model is presented in which lipid hydrogen comes from NADPH produced in PS1, NADPH produced by OPP, and intracellular water. With published values or best estimates of the fractionation factors for these sources (αPS1 = 0.4, αOPP = 0.75, and αH2O = 0) and half of the hydrogen in a lipid derived from water the model indicates αlipid = 0.79. This value is within the range measured for alkenones (αalkenone = 0.77 to 0.81) and fatty acids (αFA = 0.75 to 0.82) in the chemostat cultures, but is greater than the range for brassicasterol (αbrassicasterol = 0.68 to 0.72). The latter is attributed to a greater proportion of hydrogen from NADPH relative to water in isoprenoid lipids. The model successfully explains the increase in 2H/1H fractionation in the sterol 24-methyl-cholesta-5,24(28)-dien-3β-ol from marine centric diatom T. pseudonana chemostat cultures as growth rate increases. Insensitivity of αFA in those same cultures may be attributable to a larger fraction of hydrogen in fatty acids sourced from intracellular water at the expense of NADPH as growth rate increases. The high sensitivity of α to growth rate in E. huxleyi lipids and a T. pseudonana sterol implies that any change in growth rate larger than ~0.15 div d-1 can cause a change in δ2Hlipid that is larger than the analytical error of the measurement (~5‰), and needs to be considered when interpreting δ2Hlipid variations in sediments. PMID:26576007

The Influence of Growth Rate on 2H/1H Fractionation in Continuous Cultures of the Coccolithophorid Emiliania huxleyi and the Diatom Thalassiosira pseudonana.

PubMed

Sachs, Julian P; Kawka, Orest E

2015-01-01

The hydrogen isotope (2H/1H) ratio of lipids from phytoplankton is a powerful new tool for reconstructing hydroclimate variations in the geologic past from marine and lacustrine sediments. Water 2H/1H changes are reflected in lipid 2H/1H changes with R2 > 0.99, and salinity variations have been shown to cause about a 1‰ change in lipid δ2H values per unit (ppt) change in salinity. Less understood are the effects of growth rate, nutrient limitation and light on 2H/1H fractionation in phytoplankton. Here we present the first published study of growth rate effects on 2H/1H fractionation in the lipids of coccolithophorids grown in continuous cultures. Emiliania huxleyi was cultivated in steady state at four growth rates and the δ2H value of individual alkenones (C37:2, C37:3, C38:2, C38:3), fatty acids (C14:0, C16:0, C18:0), and 24-methyl cholest-5,22-dien-3β-ol (brassicasterol) were measured. 2H/1H fractionation increased in all lipids as growth rate increased by 24‰ to 79‰ (div d-1)-1. We attribute this response to a proportional increase in the fraction of NADPH from Photosystem I (PS1) of photosynthesis relative to NADPH from the cytosolic oxidative pentose phosphate (OPP) pathway in the synthesis of lipids as growth rate increases. A 3-endmember model is presented in which lipid hydrogen comes from NADPH produced in PS1, NADPH produced by OPP, and intracellular water. With published values or best estimates of the fractionation factors for these sources (αPS1 = 0.4, αOPP = 0.75, and αH2O = 0) and half of the hydrogen in a lipid derived from water the model indicates αlipid = 0.79. This value is within the range measured for alkenones (αalkenone = 0.77 to 0.81) and fatty acids (αFA = 0.75 to 0.82) in the chemostat cultures, but is greater than the range for brassicasterol (αbrassicasterol = 0.68 to 0.72). The latter is attributed to a greater proportion of hydrogen from NADPH relative to water in isoprenoid lipids. The model successfully explains the increase in 2H/1H fractionation in the sterol 24-methyl-cholesta-5,24(28)-dien-3β-ol from marine centric diatom T. pseudonana chemostat cultures as growth rate increases. Insensitivity of αFA in those same cultures may be attributable to a larger fraction of hydrogen in fatty acids sourced from intracellular water at the expense of NADPH as growth rate increases. The high sensitivity of α to growth rate in E. huxleyi lipids and a T. pseudonana sterol implies that any change in growth rate larger than ~0.15 div d-1 can cause a change in δ2Hlipid that is larger than the analytical error of the measurement (~5‰), and needs to be considered when interpreting δ2Hlipid variations in sediments.

A Comparison of Attitudes and Final Grades among Freshman Dental Students.

ERIC Educational Resources Information Center

Lee, Mickey M.; And Others

1981-01-01

A study examined students' change in attitudes toward dental education, themselves, and gross anatomy based on their experience in a difficult anatomy course and their final grades. Change occurred only in their attitudes about dental education, but it is concluded that specific aspects of the environment can be used to predict a final grade. (MSE)

Final Report to the Clean Air Act Advisory Committee, Title V Implementation Experience

EPA Pesticide Factsheets

In 2004, the Clean Air Act Advisory Committee established the Task Force on Title V Implementation Experience to report on stakeholder experience with implementation of the Title V operating permit program. This report details their recommendations.

From access to success in science: An academic-student affairs intervention for undergraduate freshmen biology students

NASA Astrophysics Data System (ADS)

Aldridge, Jacqueline Nouvelle

The first year experience is known to present an array of challenges for traditional college students. In particular, freshmen who major in a STEM discipline have their own unique set of challenges when they transition from high school science and math to college science and math; especially chemistry. As a result, students may encounter negative experiences which lower academic and social confidence. This project was designed as a pilot study intervention for a small group of freshmen biology students who were considered academically at-risk due their math SAT scores. The study occurred during the fall semester involving an enhanced active learning component based on the Peer-led Team Learning (PLTL) general chemistry supplemental pedagogy model, and a biology-focused First Year Experience (FYE). PLTL workshops took place in freshmen residence halls, creating a live-n-learn community environment. Mid-term and final chemistry grades and final math grades were collected to measure academic progress. Self-reporting surveys and journals were used to encourage participants to reconstruct their experiences and perceptions of the study. Descriptive analysis was performed to measure statistical significance between midterm and final grade performance, and a general inductive qualitative method was used to determine academic and social confidence as well as experiences and perceptions of the project. Findings of this project revealed a statistically significant improvement between chemistry midterm and final grades of the sample participants. Although academic confidence did not increase, results reveal that social confidence progressed as the majority of students developed a value for studying in groups.

MSFC Skylab corollary experiments

NASA Technical Reports Server (NTRS)

1974-01-01

The evolution of the development and integration of Skylab experiments from initial concepts through mission operations is documented. All experiment systems are covered as well as management controls which were developed and exercised to assure acceptable operational capability and optimize data acquisition for final scientific results.

On the placement of practice questions during study.

PubMed

Weinstein, Yana; Nunes, Ludmila D; Karpicke, Jeffrey D

2016-03-01

Retrieval practice improves retention of information on later tests. A question remains: When should retrieval occur during learning-interspersed throughout study or at the end of each study period? In a lab experiment, an online experiment, and a classroom study, we aimed to determine the ideal placement (interspersed vs. at-the-end) of retrieval practice questions. In the lab experiment, 64 subjects viewed slides about APA style and answered short-answer practice questions about the content or restudied the slides (restudy condition). The practice questions either appeared 1 every 1-2 slides (interspersed condition), or all at the end of the presentation (at-the-end condition). One week later, subjects returned and answered the same questions on a final test. In the online experiment, 175 subjects completed the same procedure. In the classroom study, 62 undergraduate students took quizzes as part of class lectures. Short-answer practice questions appeared either throughout the lectures (interspersed condition) or at the end of the lectures (at-the-end condition). Nineteen days after the last quiz, students were given a surprise final test. Results from the 3 experiments converge in demonstrating an advantage for interspersing practice questions on the initial tests, but an absence of this advantage on the final test. (c) 2016 APA, all rights reserved).

DIME Students Discuss Final Drop Tower Experiment Design

NASA Technical Reports Server (NTRS)

2002-01-01

Students discuss fine points of their final design for the Drop Tower experiment during the second Dropping in a Microgravity Environment (DIME) competition held April 23-25, 2002, at NASA's Glenn Research Center. Competitors included two teams from Sycamore High School, Cincinnati, OH, and one each from Bay High School, Bay Village, OH, and COSI Academy, Columbus, OH. DIME is part of NASA's education and outreach activities. Details are on line at http://microgravity.grc.nasa.gov/DIME_2002.html.

Generation and focusing of pulsed intense ion beams: Final report, 1 July 1987--30 September 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammer, D.A.; Kusse, B.R.; Sudan, R.N.

1989-08-03

This paper discusses the following experiments: ion diode experiments at 0.5 /times/ 10/sup 12/ W on the LION accelerator; spectroscopic studies of ion diodes; ion beam-plasma channel transport research; and plasma opening switch experiments.

Analysis of Time-Series Quasi-Experiments. Final Report.

ERIC Educational Resources Information Center

Glass, Gene V.; Maguire, Thomas O.

The objective of this project was to investigate the adequacy of statistical models developed by G. E. P. Box and G. C. Tiao for the analysis of time-series quasi-experiments: (1) The basic model developed by Box and Tiao is applied to actual time-series experiment data from two separate experiments, one in psychology and one in educational…

Acquisition of He3 Cryostat Insert for Experiments on Topological Insulators

DTIC Science & Technology

2016-02-03

facilitated transport experiments on topological insulators and Dirac and Weyl semimetals. These experiments resulted in several notable achievements and...Approved for Public Release; Distribution Unlimited Final Report: Acquisition of He3 Cryostat Insert for Experiments on Topological Insulators . The views...Experiments on Topological Insulators . Report Title The award enabled the PI to acquire a complete cryogenic system with a 9-Tesla superconducting magnet. The

Infants Learn Phonotactic Regularities from Brief Auditory Experience.

ERIC Educational Resources Information Center

Chambers, Kyle E.; Onishi, Kristine H.; Fisher, Cynthia

2003-01-01

Two experiments investigated whether novel phonotactic regularities, not present in English, could be acquired by 16.5-month-olds from brief auditory experience. Subjects listened to consonant-vowel-consonant syllables in which particular consonants were artificially restricted to either initial or final position. Findings in a subsequent…

Medical students in their final six months of training: progress in self-perceived clinical competence, and relationship between experience and confidence in practical skills.

PubMed

Lai, N M; Sivalingam, N; Ramesh, J C

2007-11-01

We evaluated the progress in the self-perceived competence of medical students in a range of common clinical, practical and personal skills, in their final six months of training. The study was conducted on 65 final-year medical students undertaking their senior clerkship training at International Medical University, Malaysia. Questionnaire surveys were conducted at the beginning and the end of the six-month period, with 44 items covering clinical, practical, personal skills and readiness to work. Correlations were performed for experience and self-perceived competence, with the respective skills. 64 students returned the first survey and 63 returned the second survey. When the two survey results were compared, significant increases were found in self-perceived competence for the majority of the skills examined. The items with no significant improvement were divided into those which the students were already proficient in before senior clerkship, and those in which experience and confidence remained poor at the end of training. There were significant, but moderate, correlations between the experience and confidence of all common practical skills (correlation coefficients: 0.348-0.522, p-value is less than 0.001 for all items). At the end of training, students were, in general, more prepared to work as house officers (mean rating in the first survey: 3.05, second survey: 3.97, p-value is less than 0.001). Significant progresses in clinical experience and confidence can be observed in the final stages of medical training. The findings of inadequate improvements in some skills call for dedicated training sessions and strengthening of on-site supervision.

Accelerator performance analysis of the Fermilab Muon Campus

DOE PAGES

Stratakis, Diktys; Convery, Mary E.; Johnstone, Carol; ...

2017-11-21

Fermilab is dedicated to hosting world-class experiments in search of new physics that will operate in the coming years. The Muon g-2 Experiment is one such experiment that will determine with unprecedented precision the muon anomalous magnetic moment, which offers an important test of the Standard Model. We describe in this study the accelerator facility that will deliver a muon beam to this experiment. We first present the lattice design that allows for efficient capture, transport, and delivery of polarized muon beams. We then numerically examine its performance by simulating pion production in the target, muon collection by the downstreammore » beam line optics, as well as transport of muon polarization. Lastly, we finally establish the conditions required for the safe removal of unwanted secondary particles that minimizes contamination of the final beam.« less

CFD Analysis in Advance of the NASA Juncture Flow Experiment

NASA Technical Reports Server (NTRS)

Lee, H. C.; Pulliam, T. H.; Neuhart, D. H.; Kegerise, M. A.

2017-01-01

NASA through its Transformational Tools and Technologies Project (TTT) under the Advanced Air Vehicle Program, is supporting a substantial effort to investigate the formation and origin of separation bubbles found on wing-body juncture zones. The flow behavior in these regions is highly complex, difficult to measure experimentally, and challenging to model numerically. Multiple wing configurations were designed and evaluated using Computational Fluid Dynamics (CFD), and a series of wind tunnel risk reduction tests were performed to further down-select the candidates for the final experiment. This paper documents the CFD analysis done in conjunction with the 6 percent scale risk reduction experiment performed in NASA Langley's 14- by 22-Foot Subsonic Tunnel. The combined CFD and wind tunnel results ultimately helped the Juncture Flow committee select the wing configurations for the final experiment.

75 FR 38725 - Service Performance Measurement

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-06

... of Customer Sastisfaction A. General Considerations B. Rule 3055.91--Consumer Access to Postal Services C. Rule 3055.92--Customer Experience Measurement Surveys D. Rule 3055.93--Mystery Shopper Program... Commission is adopting a final rule on service perfomance measurement and customer satisfaction. The final...

Expanded clay hot mix study : final report: part I.

DOT National Transportation Integrated Search

1969-04-01

This is part I of a two part final report on expanded clay hot mix to: (1) evaluate the use of various expanded clay bituminous mixtures under high traffic counts, (2) accumulate through experience testing, suitable information on the physical proper...

Thought Experiments in Physics Education: A Simple and Practical Example.

ERIC Educational Resources Information Center

Lattery, Mark J.

2001-01-01

Uses a Galilean thought experiment to enhance learning in a college-level physical science course. Presents both modern and historical perspectives of Galileo's work. As a final project, students explored Galileo's thought experiment in the laboratory using modern detectors with satisfying results. (Contains 25 references.) (Author/ASK)

Emotional Intelligence in Intensive Clinical Experiences for Nursing Students

ERIC Educational Resources Information Center

Zoromski, Lorraine M.

2017-01-01

This study looked for associations between measures of emotional intelligence in an intensive clinical experience for nursing students in their final semester of an associate's degree program. The theory of emotional labor was used to make connections between nursing clinical experience and emotional intelligence. Twenty nursing students from a…

Status and Prospects for Hadron Production Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schroeter, Raphaeel

2010-03-30

The latest results from the HARP, MIPP and NA61 Hadron Production Experiments are reviewed and their implications for neutrinos physics experiments are discussed. We emphasize three neutrino sources: accelerator-based neutrino beams, advanced neutrino sources and atmospheric neutrinos. Finally, prospects from additional forthcoming hadron production measurements are presented.

Development of an Energetic X-Ray Imaging Telescope Experiment (EXITE) and Associated Balloon Gondola System

NASA Technical Reports Server (NTRS)

1997-01-01

This is the Final Report for grant NAGW-624, which was our original grant to develop the Energetic X- ray Imaging Telescope Experiment (EXITE) and Associated Balloon Gondola. The EXITE grant was changed over to a new grant (from GSFC), NAG5-5103, beginning in FY97 and is currently very much continuing under that grant. The Final Report presented here then covers the EXITE development under the original grant, which in fact continued (with a 1 year no-cost extension) through December 31, 1997.

Perspectives of Canadian Final-Year Physiotherapy Students on Cardiorespiratory Physiotherapy as a Career Choice

PubMed Central

Araujo, Tamara; Romano, Julia Marie; Camp, Pat G.; Hall, Mark; Mathur, Sunita; Brooks, Dina

2016-01-01

Purpose: To investigate the opinions of final-year Canadian physiotherapy students of cardiorespiratory physiotherapy (CRP) and the factors influencing their decision about whether to pursue a career in CRP. Methods: A cross-sectional online survey was completed by final-year Master of Science of Physical Therapy students from three of the largest English-speaking physiotherapy schools in Canada. Results: A total of 120 students responded to the survey (overall response rate was 44%). Fifteen students (12.5%) responded that they were extremely or quite interested in specializing in CRP. The most common factors that positively influenced students' decision to consider specializing in CRP were job accessibility, potential salary, and experiences in the area, and the most common factors that negatively influenced their decision were the clinical aspects of the area, their experiences in the area, job accessibility, and the influence of others. The most common factors that positively influenced students' opinion of CRP were their clinical supervisor, educator, or lecturer; their own clinical experience; and evidence in the literature, and the most common factors that negatively influenced their opinion were their own clinical experience and their peers. Conclusion: Strategies focusing on increasing awareness of the role of physiotherapists in the care of patients with cardiorespiratory conditions, exposing students to the positive impact that physiotherapists have in this practice area, and good mentorship experiences may promote the attractiveness of this specialty. PMID:27909378

Training presence: the importance of virtual reality experience on the "sense of being there".

PubMed

Gamito, Pedro; Oliveira, Jorge; Morais, Diogo; Baptista, André; Santos, Nuno; Soares, Fábio; Saraiva, Tomaz; Rosa, Pedro

2010-01-01

Nature and origin of presence are still unclear. Although it can be characterized, under a neurophysiological perspective, as a process resulting from a synchrony between cognitive and perceptive systems, the multitude of associated processes reduces the chances of brain mapping presence. In this way, our study was designed in order to understand the possible role of VR experience on presence in a virtual environment. For our study, 16 participants (M=28.39 years; SD=13.44) of both genders without computer experience were selected. The study design consisted of two assessments (initial and final), where the participants were evaluated with BFI, PQ, ITQ, QC, MCSDS-SF, STAI, visual attention and behavioral measures after playing an first person shooter (FPS) game. In order to manipulate the level of VR experience the participants were trained on, a different FPS was used during the 12 weekly sessions of 30 minutes. Results revealed significant differences between the first and final assessment for presence (F(1,15)=11.583; MSE=775.538; p<01) and immersion scores (F(1,15)=6.234; MSE=204.962; p<05), indicating higher levels of presence and immersion in the final assessment. No statistical significant results were obtained for cybersickness or the behavioral measures. In summary, our results showed that training and the subsequent higher computer experience levels can increase immersion and presence.

Apollo-Soyuz test project: Composite of MSFC final science report

NASA Technical Reports Server (NTRS)

1977-01-01

Experimental procedures of nine experiments conducted during the Apollo-Soyuz Test Project mission from July 15th to July 24th, 1975 are presented. Conclusions and recommendations based on these experiments are given.

R-X Modeling Figures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goda, Joetta Marie; Miller, Thomas; Grogan, Brandon

2016-10-26

This document contains figures that will be included in an ORNL final report that details computational efforts to model an irradiation experiment performed on the Godiva IV critical assembly. This experiment was a collaboration between LANL and ORNL.

Description of the Large-Gap Magnetic Suspension System (LGMSS) ground based experiment

NASA Technical Reports Server (NTRS)

Groom, Nelson J.

1991-01-01

An overview of the Large Gap Magnetic Suspension System (LGMSS) ground-based experiment is provided. A description of the experiment, as originally defined, and the experiment objectives and potential applications of the technology resulting from the experiment are presented. Also, the results of two studies which were conducted to investigate the feasibility of implementing the experiment are presented and discussed. Finally, a description of the configuration which was selected for the experiment is described, and a summary of the paper is presented.

Analysis of stability to cheaters in models of antibiotic degrading microbial communities.

PubMed

Szilágyi, András; Boza, Gergely; Scheuring, István

2017-06-21

Antibiotic resistance carried out by antibiotic degradation has been suggested recently as a new mechanism to maintain coexistence of microbial species competing on a single limiting resource, even in well-mixed homogeneous environments. Species diversity and community stability, however, critically depend on resistance against social cheaters, mutants that do not invest in production, but still enjoy the benefits provided by others. Here we investigate how different mutant cheaters affect the stability of antibiotic producing and degrading microbial communities. We consider two cheater types, production and degradation cheaters. We generalize the mixed inhibition-zone and chemostat models introduced previously [Kelsic, E. D., Zhao, J., Vetsigian, K., Kishony, R., 2015. Counteraction of an tibiotic production and degradation stabilizes microbial communities. Nature521, 516-519.] to study the population dynamics of microbial communities in well-mixed environment, and analyze the invasion of different cheaters in these models. We show that production cheaters, mutants that cease producing antibiotics, always destroy coexistence whenever there is a cost of producing these antibiotics. Degradation cheaters, mutants that loose their function of producing extracellular antibiotic degrading molecules, induce community collapse only if the cost of producing the degradation factors is above a critical level. Our analytical studies, supported by numerical simulations, highlight the sensitivity of antibiotic producing and degrading communities to loss-of-function mutants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Replacement of the initial steps of ethanol metabolism in Saccharomyces cerevisiae by ATP-independent acetylating acetaldehyde dehydrogenase

PubMed Central

Kozak, Barbara U.; van Rossum, Harmen M.; Niemeijer, Matthijs S.; van Dijk, Marlous; Benjamin, Kirsten; Wu, Liang; Daran, Jean-Marc G.; Pronk, Jack T.

2016-01-01

In Saccharomyces cerevisiae ethanol dissimilation is initiated by its oxidation and activation to cytosolic acetyl-CoA. The associated consumption of ATP strongly limits yields of biomass and acetyl-CoA-derived products. Here, we explore the implementation of an ATP-independent pathway for acetyl-CoA synthesis from ethanol that, in theory, enables biomass yield on ethanol that is up to 40% higher. To this end, all native yeast acetaldehyde dehydrogenases (ALDs) were replaced by heterologous acetylating acetaldehyde dehydrogenase (A-ALD). Engineered Ald− strains expressing different A-ALDs did not immediately grow on ethanol, but serial transfer in ethanol-grown batch cultures yielded growth rates of up to 70% of the wild-type value. Mutations in ACS1 were identified in all independently evolved strains and deletion of ACS1 enabled slow growth of non-evolved Ald− A-ALD strains on ethanol. Acquired mutations in A-ALD genes improved affinity—Vmax/Km for acetaldehyde. One of five evolved strains showed a significant 5% increase of its biomass yield in ethanol-limited chemostat cultures. Increased production of acetaldehyde and other by-products was identified as possible cause for lower than theoretically predicted biomass yields. This study proves that the native yeast pathway for conversion of ethanol to acetyl-CoA can be replaced by an engineered pathway with the potential to improve biomass and product yields. PMID:26818854

River mixing in the Amazon as a driver of concentration-discharge relationships

NASA Astrophysics Data System (ADS)

Moquet, Jean-Sébastien; Bouchez, Julien; Carlo Espinoza, Jhan; Martinez, Jean-Michel; Guyot, Jean-Loup; Lagane, Christelle; Filizola, Naziano; Aniceto, Keila; Noriega, Luis; Hidalgo Sanchez, Liz; Pombosa, Rodrigo; Fraizy, Pascal; Santini, William; Timouk, Franck; Vauchel, Philippe

2017-04-01

Large hydrological systems such as continental-scale river basins aggregate water from compositionally different tributaries. Here we explore how such aggregation can affect solute concentration-discharge (C-Q) relationships and thus obscure the message carried by these relationships in terms of weathering properties of the Critical Zone. We compute 10 day-frequency time series of Q and major solute (Si, Ca2+, Mg2+, K+, Na+, Cl-, SO42-) C and fluxes (F) for 13 gauging stations of the SNO-HYBAM Monitoring Program (Geodynamical, hydrological and Biogeochemical control of erosion/weathering and material transport in the Amazon, Orinoco and Congo basins) located throughout the Amazon basin, the largest river basin in the world. Concentration-discharge relationships vary in a systematic manner, shifting for most solutes from a nearly "chemostatic" behavior (constant C) at the Andean mountain front to a more "dilutional" pattern (negative C-Q relationship) towards the system mouth. Associated to this shift in trend is a shift in shape: C-Q hysteresis becomes more prominent at the most downstream stations. A simple model of tributary mixing allows us to identify the important parameters controlling C-Q trends and shapes in the mixture, and we show that for the Amazon case, the model results are in qualitative agreement with the observations. Altogether, this study suggests that mixing of water and solutes between different flowpaths leads to altered C-Q relationships.

A model for light distribution and average solar irradiance inside outdoor tubular photobioreactors for the microalgal mass culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernandez, F.G.A.; Camacho, F.G.; Perez, J.A.S.

1997-09-05

A mathematical model to estimate the solar irradiance profile and average light intensity inside a tubular photobioreactor under outdoor conditions is proposed, requiring only geographic, geometric, and solar position parameters. First, the length of the path into the culture traveled by any direct or disperse ray of light was calculated as the function of three variables: day of year, solar hour, and geographic latitude. Then, the phenomenon of light attenuation by biomass was studied considering Lambert-Beer`s law (only considering absorption) and the monodimensional model of Cornet et al. (1900) (considering absorption and scattering phenomena). Due to the existence of differentialmore » wavelength absorption, none of the literature models are useful for explaining light attenuation by the biomass. Therefore, an empirical hyperbolic expression is proposed. The equations to calculate light path length were substituted in the proposed hyperbolic expression, reproducing light intensity data obtained in the center of the loop tubes. The proposed model was also likely to estimate the irradiance accurately at any point inside the culture. Calculation of the local intensity was thus extended to the full culture volume in order to obtain the average irradiance, showing how the higher biomass productivities in a Phaeodactylum tricornutum UTEX 640 outdoor chemostat culture could be maintained by delaying light limitation.« less

Effects of substrate concentrations on the growth of heterotrophic bacteria and algae in secondary facultative ponds.

PubMed

Kayombo, S; Mbwette, T S A; Katima, J H Y; Jorgensen, S E

2003-07-01

This paper presents the effect of substrate concentration on the growth of a mixed culture of algae and heterotrophic bacteria in secondary facultative ponds (SFPs) utilizing settled domestic sewage as a sole source of organic carbon. The growth of the mixed culture was studied at the concentrations ranging between 200 and 800 mg COD/l in a series of batch chemostat reactors. From the laboratory data, the specific growth rate (micro) was determined using the modified Gompertz model. The maximum specific growth rate ( micro(max)) and half saturation coefficients (K(s)) were calculated using the Monod kinetic equation. The maximum observed growth rate ( micro(max)) for heterotrophic bacteria was 3.8 day(-1) with K(s) of 200 mg COD/l. The micro(max) for algal biomass based on suspended volatile solids was 2.7 day(-1) with K(s) of 110 mg COD/l. The micro(max) of algae based on the chlorophyll-a was 3.5 day(-1) at K(s) of 50mg COD/l. The observed specific substrate removal by heterotrophic bacteria varied between the concentrations of substrate used and the average value was 0.82 (mg COD/mg biomass). The specific substrate utilization rate in the bioreactors was direct proportional to the specific growth rate. Hence, the determined Monod kinetic parameters are useful for the definition of the operation of SFPs.

Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon

PubMed Central

Curran, Thomas D; Abacha, Fatima; Hibberd, Stephen P; Green, Jeffrey

2017-01-01

SlyA is a member of the MarR family of bacterial transcriptional regulators. Previously, SlyA has been shown to directly regulate only two operons in Escherichia coli K-12 MG1655, fimB and hlyE (clyA). In both cases, SlyA activates gene expression by antagonizing repression by the nucleoid-associated protein H-NS. Here, the transcript profiles of aerobic glucose-limited steady-state chemostat cultures of E. coli K-12 MG1655, slyA mutant and slyA over-expression strains are reported. The transcript profile of the slyA mutant was not significantly different from that of the parent; however, that of the slyA expression strain was significantly different from that of the vector control. Transcripts representing 27 operons were increased in abundance, whereas 3 were decreased. Of the 30 differentially regulated operons, 24 have previously been associated with sites of H-NS binding, suggesting that antagonism of H-NS repression is a common feature of SlyA-mediated transcription regulation. Direct binding of SlyA to DNA located upstream of a selection of these targets permitted the identification of new operons likely to be directly regulated by SlyA. Transcripts of four operons coding for cryptic adhesins exhibited enhanced expression, and this was consistent with enhanced biofilm formation associated with the SlyA over-producing strain. PMID:28073397

Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon.

PubMed

Curran, Thomas D; Abacha, Fatima; Hibberd, Stephen P; Rolfe, Matthew D; Lacey, Melissa M; Green, Jeffrey

2017-03-01

SlyA is a member of the MarR family of bacterial transcriptional regulators. Previously, SlyA has been shown to directly regulate only two operons in Escherichia coli K-12 MG1655, fimB and hlyE (clyA). In both cases, SlyA activates gene expression by antagonizing repression by the nucleoid-associated protein H-NS. Here, the transcript profiles of aerobic glucose-limited steady-state chemostat cultures of E. coli K-12 MG1655, slyA mutant and slyA over-expression strains are reported. The transcript profile of the slyA mutant was not significantly different from that of the parent; however, that of the slyA expression strain was significantly different from that of the vector control. Transcripts representing 27 operons were increased in abundance, whereas 3 were decreased. Of the 30 differentially regulated operons, 24 have previously been associated with sites of H-NS binding, suggesting that antagonism of H-NS repression is a common feature of SlyA-mediated transcription regulation. Direct binding of SlyA to DNA located upstream of a selection of these targets permitted the identification of new operons likely to be directly regulated by SlyA. Transcripts of four operons coding for cryptic adhesins exhibited enhanced expression, and this was consistent with enhanced biofilm formation associated with the SlyA over-producing strain.

Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome

PubMed Central

Mosleth, Ellen F.; Rud, Ida; Branco dos Santos, Filipe; Snipen, Lars; Liland, Kristian Hovde

2017-01-01

Effects of glucose availability were investigated in Lactobacillus sakei strains 23K and LS25 cultivated in anaerobic, glucose-limited chemostats set at high (D = 0.357 h-1) and low (D = 0.045 h-1) dilution rates. We observed for both strains a shift from homolactic towards more mixed acid fermentation when comparing high to low growth rates. However, this change was more pronounced for LS25 than for 23K, where dominating products were lactate>formate>acetate≥ethanol at both conditions. A multivariate approach was used for analyzing proteome and transcriptome data from the bacterial cultures, where the predictive power of the omics data was used for identifying features that can explain the differences in the end-product profiles. We show that the different degree of response to the same energy restriction revealed interesting strain specific regulation. An elevated formate production level during slow growth, more for LS25 than for 23K, was clearly reflected in correlating pyruvate formate lyase expression. With stronger effect for LS25, differential expression of the Rex transcriptional regulator and NADH oxidase, a target of Rex, indicated that maintainance of the cell redox balance, in terms of the NADH/NAD+ ratio, may be a key process during the metabolic change. The results provide a better understanding of different strategies that cells may deploy in response to changes in substrate availability. PMID:29099858

A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

PubMed

Draghi, W O; Del Papa, M F; Hellweg, C; Watt, S A; Watt, T F; Barsch, A; Lozano, M J; Lagares, A; Salas, M E; López, J L; Albicoro, F J; Nilsson, J F; Torres Tejerizo, G A; Luna, M F; Pistorio, M; Boiardi, J L; Pühler, A; Weidner, S; Niehaus, K; Lagares, A

2016-07-11

Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia.

A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti

PubMed Central

Draghi, W. O.; Del Papa, M. F.; Hellweg, C.; Watt, S. A.; Watt, T. F.; Barsch, A.; Lozano, M. J.; Lagares, A.; Salas, M. E.; López, J. L.; Albicoro, F. J.; Nilsson, J. F.; Torres Tejerizo, G. A.; Luna, M. F.; Pistorio, M.; Boiardi, J. L.; Pühler, A.; Weidner, S.; Niehaus, K.; Lagares, A.

2016-01-01

Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0–6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia. PMID:27404346

Enrichment of DNRA bacteria in a continuous culture

PubMed Central

van den Berg, Eveline M; van Dongen, Udo; Abbas, Ben; van Loosdrecht, Mark CM

2015-01-01

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are competing microbial nitrate-reduction processes. The occurrence of DNRA has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in a laboratory reactor, yet no successful DNRA enrichment culture has been described. We showed that a stable DNRA-dominated enrichment culture can be obtained in a chemostat system. The enrichment was based on the hypothesis that nitrate limitation is the dominant factor in selecting for DNRA. First, a conventional denitrifying culture was enriched from activated sludge, with acetate and nitrate as substrates. Next, the acetate concentration in the medium was increased to obtain nitrate-limiting conditions. As a result, conversions shifted from denitrification to DNRA. In this selection of a DNRA culture, two important factors were the nitrate limitation and a relatively low dilution rate (0.026 h−1). The culture was a highly enriched population of Deltaproteobacteria most closely related to Geobacter lovleyi, based on 16S rRNA gene sequencing (97% similarity). We established a stable and reproducible cultivation method for the enrichment of DNRA bacteria in a continuously operated reactor system. This enrichment method allows to further investigate the DNRA process and address the factors for competition between DNRA and denitrification, or other N-conversion pathways. PMID:25909972

Human acylphosphatase cannot replace phosphoglycerate kinase in Saccharomyces cerevisiae.

PubMed

Van Hoek, P; Modesti, A; Ramponi, G; Kötter, P; van Dijken, J P; Pron, J T

2001-10-01

Human acylphosphatase (h-AP, EC 3.6.1.7) has been reported to catalyse the hydrolysis of the 1-phosphate group of 1,3-diphosphoglycerate. In vivo operation of this reaction in the yeast Saccharomyces cerevisiae would bypass phosphoglycerate kinase and thus reduce the ATP yield from glycolysis. To investigate whether h-AP can indeed replace the S. cerevisiae phosphoglycerate kinase, a multi-copy plasmid carrying the h-AP gene under control of the yeast TDH3 promoter was introduced into a pgk1 delta mutant of S. cerevisiae. A strain carrying the expression vector without the h-AP cassette was used as a reference. For both strains, steady-state carbon- and energy-limited chemostat cultures were obtained at a dilution rate of 0.10 h(-1) on a medium containing a mixture of glucose and ethanol (15% and 85% on a carbon basis, respectively). Although the h-AP strain exhibited a high acylphosphatase activity in cell extracts, switching to glucose as sole carbon and energy source resulted in a complete arrest of glucose consumption and growth. The lack of a functional glycolytic pathway was further evident from the absence of ethanol formation in the presence of excess glucose in the culture. As h-AP cannot replace yeast phosphoglycerate kinase in vivo, the enzyme is not a useful tool to modify the ATP yield of glycolysis in S. cerevisiae.

Analysis of the Aspergillus fumigatus proteome reveals metabolic changes and the activation of the pseurotin A biosynthesis gene cluster in response to hypoxia.

PubMed

Vödisch, Martin; Scherlach, Kirstin; Winkler, Robert; Hertweck, Christian; Braun, Hans-Peter; Roth, Martin; Haas, Hubertus; Werner, Ernst R; Brakhage, Axel A; Kniemeyer, Olaf

2011-05-06

The mold Aspergillus fumigatus is the most important airborne fungal pathogen. Adaptation to hypoxia represents an important virulence attribute for A. fumigatus. Therefore, we aimed at obtaining a comprehensive overview about this process on the proteome level. To ensure highly reproducible growth conditions, an oxygen-controlled, glucose-limited chemostat cultivation was established. Two-dimensional gel electrophoresis analysis of mycelial and mitochondrial proteins as well as two-dimensional Blue Native/SDS-gel separation of mitochondrial membrane proteins led to the identification of 117 proteins with an altered abundance under hypoxic in comparison to normoxic conditions. Hypoxia induced an increased activity of glycolysis, the TCA-cycle, respiration, and amino acid metabolism. Consistently, the cellular contents in heme, iron, copper, and zinc increased. Furthermore, hypoxia induced biosynthesis of the secondary metabolite pseurotin A as demonstrated at proteomic, transcriptional, and metabolite levels. The observed and so far not reported stimulation of the biosynthesis of a secondary metabolite by oxygen depletion may also affect the survival of A. fumigatus in hypoxic niches of the human host. Among the proteins so far not implicated in hypoxia adaptation, an NO-detoxifying flavohemoprotein was one of the most highly up-regulated proteins which indicates a link between hypoxia and the generation of nitrosative stress in A. fumigatus.

Déjà Vu Experiences in Healthy Czech Adults.

PubMed

Lacinová, Lenka; Neužilová Michalčáková, Radka; Širůček, Jan; Ježek, Stanislav; Chromec, Jakub; Masopustová, Zuzana; Urbánek, Tomáš; Brázdil, Milan

2016-12-01

The study examines the prevalence of déjà vu in healthy Czech adults and explores its relationships with a number of variables: age, sex, neuroticism, depression, the degree of irritability in the limbic system, perceived stress, and finally attachment avoidance and anxiety. The participants were 365 healthy adults ranging from 18 to 70 years recruited in the Czech Republic (mean age = 29.05; SD = 11.17) who filled out online questionnaires. Déjà vu experiences were reported by 324 (88.8%) of them. Persons who experienced déjà vu were younger than the persons who had not experienced it. We found that sex, levels of neuroticism, depression, perceived stress, and attachment did not serve as predictors of experiences of déjà vu phenomena. Finally, those who had reported déjà vu experiences reported more limbic system irritability symptoms. We discuss the possibility that déjà vu reports together with other studied variables mainly reflect the participants' willingness to report "extraordinal" experiences.

Searching for a dark photon with DarkLight

DOE PAGES

Corliss, R.

2016-07-30

Here, we describe the current status of the DarkLight experiment at Jefferson Laboratory. DarkLight is motivated by the possibility that a dark photon in the mass range 10 to 100 MeV/c 2 could couple the dark sector to the Standard Model. DarkLight will precisely measure electron proton scattering using the 100 MeV electron beam of intensity 5 mA at the Jefferson Laboratory energy recovering linac incident on a windowless gas target of molecular hydrogen. We will detect the complete final state including scattered electron, recoil proton, and e +e - pair. A phase-I experiment has been funded and is expectedmore » to take data in the next eighteen months. The complete phase-II experiment is under final design and could run within two years after phase-I is completed. The DarkLight experiment drives development of new technology for beam, target, and detector and provides a new means to carry out electron scattering experiments at low momentum transfers.« less

Peer mentored teams to support undergraduate group work in higher education

NASA Astrophysics Data System (ADS)

Cinderey, Lynn Elizabeth

This research starts with a set of practical research questions to investigate a problem which occurs in some computing undergraduate modules that use group work as part of the learning and assessment strategy. In this study final year students with experience in information systems project work and trained in team processes met with small groups of first year computing students with the aim of turning the first year project group into a team. This study seeks to explore the experience of the final year students as they take on the role of peer tutor looking at the problems they perceive within the first year teams and the skills and knowledge they use to help them. The study includes the recruitment and training of final year students (n=9) and allocation to first year teams. The final year students acted as co-researchers and team leaders in L4 Information Systems project work and recorded their thoughts and observations in a diary during the first semester of 2008/9 academic year. Diary data was supplemented by interview data from a sample of final year students (n=4). The sample was selected based on the richness of the data provided in the diaries and the number of meetings held with their teams. Rich data and thick descriptions were essential for a phenomenological examination of the experience of the final year students. A number of findings emerged. A critical approach to analysis revealed ongoing conflicts occurred across cultural divides within the first year teams that final year leaders did not articulate or appear fully aware of. This had important implications for individual team members. Other findings which relate to issues of changing levels of motivation in the teams over the ten weeks, roles adopted by the leaders, ability to systematize the project or team processes and the ability to reflect on unsuccessful strategies also had implications for peer mentoring training and support. The picture that emerged from the data suggested that lack of intercultural sensitivity and empathy within the student group reduces the value of peer mentoring interventions for some first year undergraduate team members in computing. In order to improve the experience for all students, methods to develop intercultural sensitivity within the student body are examined and a framework for training and support is proposed.

LTPP pavement maintenance materials : SHRP joint reseal experiment, final report.

DOT National Transportation Integrated Search

1999-09-01

The Strategic Highway Research Program (SHRP) H-106 maintenance experiment and the Federal Highway : Administration (FHWA) Long-Term Monitoring (LTM) of Pavement Maintenance Materials Test Sites project studied : the resealing of joints in concrete p...

Strangeness Production at COSY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hinterberger, Frank; Machner, Hartmut; Siudak, Regina

2011-10-24

The paper gives an overview of strangeness-production experiments at the Cooler Synchrotron COSY. Results on kaon-pair and {phi} meson production in pp, pd and dd collisions, hyperon-production experiments and {Lambda}p final-state interaction studies are presented.

Transportation Management For Corridors And Activity Centers: Opportunities And Experiences, Final Report

DOT National Transportation Integrated Search

1986-05-01

THIS REPORT CONSISTS OF TWO SECTIONS, TRANSPORTATION MANAGEMENT FOR CORRIDORS AND TRANSPORTATION MANAGEMENT FOR ACTIVITY CENTERS, THAT DESCRIBE TRANSPORTATION MANAGEMENT EXPERIENCES IN THE UNITED STATES. : CASE STUDIES ARE THE FOCUS OF EACH SECTIO...

The International Heat Stress Genotype Experiment for Modeling Wheat Response to Heat: Field Experiments and AgMIP-Wheat Multi-Model Simulations

NASA Technical Reports Server (NTRS)

Martre, Pierre; Reynolds, Matthew P.; Asseng, Senthold; Ewert, Frank; Alderman, Phillip D.; Cammarano, Davide; Maiorano, Andrea; Ruane, Alexander C.; Aggarwal, Pramod K.; Anothai, Jakarat;

FINAL DESIGN REVIEW REPORT Subcritical Experiments Gen 2, 3-ft Confinement Vessel Weldment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romero, Christopher

A Final Design Review (FDR) of the Subcritical Experiments (SCE) Gen 2, 3-ft. Confinement Vessel Weldment was held at Los Alamos National Laboratory (LANL) on September 14, 2017. The review was a focused review on changes only to the confinement vessel weldment (versus a system design review). The changes resulted from lessons-learned in fabricating and inspecting the current set of confinement vessels used for the SCE Program. The baseline 3-ft. confinement vessel weldment design has successfully been used (to date) for three (3) high explosive (HE) over-tests, two (2) fragment tests, and five (5) integral HE experiments. The design teammore » applied lessons learned from fabrication and inspection of these vessel weldments to enhance fit-up, weldability, inspection, and fitness for service evaluations. The review team consisted of five (5) independent subject matter experts with engineering design, analysis, testing, fabrication, and inspection experience. The« less

The Senior Year Experience. Facilitating Integration, Reflection, Closure, and Transition.

ERIC Educational Resources Information Center

Gardner, John N.; Van der Veer, Gretchen

The theme of this collection of 17 monographs is defined as the "senior year experience," that final period of the undergraduate experience leading to entry into graduate school or the workplace. Part 1, "Understanding the Unique Needs of Today's Seniors," examines the characteristics and needs of senior as they make the…

Student Experience of Final-Year Undergraduate Research Projects: An Exploration of "Research Preparedness"

ERIC Educational Resources Information Center

Shaw, Kylie; Holbrook, Allyson; Bourke, Sid

2013-01-01

During this past decade the level of interest in building research capacity has intensified in Australia and internationally, with a particular emphasis on the development of postgraduate research students, but also extending to undergraduate research experience. This study investigated the student experience across a diverse range of fourth-year…

Research needs for a better understanding of wilderness visitor experiences

Treesearch

Stephen F. McCool; Chad P. Dawson

2012-01-01

What information is needed to facilitate enhanced management of visitor experiences in wilderness? The final session of the workshop comprised a facilitated process with the 20 participants to identify research and information needs to support wilderness visitor experience management. The Wilderness Act and the previous presentations and discussions not only provided a...

Incremental Sentence Processing in Japanese: A Maze Investigation into Scrambled and Control Sentences

ERIC Educational Resources Information Center

Witzel, Jeffrey; Witzel, Naoko

2016-01-01

This study investigates preverbal structural and semantic processing in Japanese, a head-final language, using the maze task. Two sentence types were tested--simple scrambled sentences (Experiment 1) and control sentences (Experiment 2). Experiment 1 showed that even for simple, mono-clausal Japanese sentences, (1) there are online processing…

Homelessness and Work Experience: Two Years in Saint Paul. Final Report.

ERIC Educational Resources Information Center

Davis, Dennis R.

A study explored the role of work experience in addressing problems of homeless people in Saint Paul (Minnesota) during the 1989-91 grant cycles of the McKinney Job Training for the Homeless Demonstration Program. The program included a number of elements: outreach, intake, assessment and enrollment, orientation, work experience, basic…

Speed Listening: Exploring an Analogue of Speed Reading. Final Report.

ERIC Educational Resources Information Center

Wallace, William P.

To determine whether the impressive rates for speed reading (e.g., 500 words per minute) can be approximated in speed listening, two experiments compared the comprehension level of material heard at a normal speaking rate with that heard at accelerated rates. In the first experiment, the major demonstration experiment, three groups of college…

Final state interactions and inclusive nuclear collisions

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Dubey, Rajendra R.

1993-01-01

A scattering formalism is developed in a multiple scattering model to describe inclusive momentum distributions for high-energy projectiles. The effects of final state interactions on response functions and momentum distributions are investigated. Calculations for high-energy protons that include shell model response functions are compared with experiments.

Prediction in the service of comprehension: modulated early brain responses to omitted speech segments.

PubMed

Bendixen, Alexandra; Scharinger, Mathias; Strauß, Antje; Obleser, Jonas

2014-04-01

Speech signals are often compromised by disruptions originating from external (e.g., masking noise) or internal (e.g., inaccurate articulation) sources. Speech comprehension thus entails detecting and replacing missing information based on predictive and restorative neural mechanisms. The present study targets predictive mechanisms by investigating the influence of a speech segment's predictability on early, modality-specific electrophysiological responses to this segment's omission. Predictability was manipulated in simple physical terms in a single-word framework (Experiment 1) or in more complex semantic terms in a sentence framework (Experiment 2). In both experiments, final consonants of the German words Lachs ([laks], salmon) or Latz ([lats], bib) were occasionally omitted, resulting in the syllable La ([la], no semantic meaning), while brain responses were measured with multi-channel electroencephalography (EEG). In both experiments, the occasional presentation of the fragment La elicited a larger omission response when the final speech segment had been predictable. The omission response occurred ∼125-165 msec after the expected onset of the final segment and showed characteristics of the omission mismatch negativity (MMN), with generators in auditory cortical areas. Suggestive of a general auditory predictive mechanism at work, this main observation was robust against varying source of predictive information or attentional allocation, differing between the two experiments. Source localization further suggested the omission response enhancement by predictability to emerge from left superior temporal gyrus and left angular gyrus in both experiments, with additional experiment-specific contributions. These results are consistent with the existence of predictive coding mechanisms in the central auditory system, and suggestive of the general predictive properties of the auditory system to support spoken word recognition. Copyright © 2014 Elsevier Ltd. All rights reserved.

U.S. Biomedical Experiments In A Soviet Biosatellite

NASA Technical Reports Server (NTRS)

Connolly, J.; Grindeland, R.; Ballard, R.

1992-01-01

NASA technical memorandum contains final report on number of U.S. experiments, mainly biomedical experiments on rats, carried out aboard Soviet Biosatellite Cosmos 1887. Satellite launched on September 29, 1987, and recovered on October 12, 1987. More than 50 NASA-sponsored scientists from Ames Research Center and from universities throughout the United States involved directly in 26 U.S./U.S.S.R. experiments.

Avoidance of Timeout from Response-Independent Food: Effects of Delivery Rate and Quality

ERIC Educational Resources Information Center

Richardson, Joseph V.; Baron, Alan

2008-01-01

In three experiments, a rat's lever presses could postpone timeouts from food pellets delivered on response-independent schedules. In Experiment 1, the pellets were delivered at variable-time (VT) rates ranging from VT 0.5 to VT 8 min. Experiment 2 replicated the VT 1 min and VT 8 min conditions of Experiment 1 with new subjects. Finally, subjects…

When pretesting fails to enhance learning concepts from reading texts.

PubMed

Hausman, Hannah; Rhodes, Matthew G

2018-05-03

Prior research suggests that people can learn more from reading a text when they attempt to answer pretest questions first. Specifically, pretests on factual information explicitly stated in a text increases the likelihood that participants can answer identical questions after reading than if they had not answered pretest questions. Yet, a central goal of education is to develop deep conceptual understanding. The present experiments investigated whether conceptual pretests facilitate learning concepts from reading texts. In Experiment 1, participants were given factual or conceptual pretest questions; a control group was not given a pretest. Participants then read a passage and took a final test consisting of both factual and conceptual questions. Some of the final test questions were repeated from the pretest and some were new. Although factual pretesting improved learning for identical factual questions, conceptual pretesting did not enhance conceptual learning. Conceptual pretest errors were significantly more likely to be repeated on the final test than factual pretest errors. Providing correct answers (Experiment 2) or correct/incorrect feedback (Experiment 3) following pretest questions enhanced performance on repeated conceptual test items, although these benefits likely reflect memorization and not conceptual understanding. Thus, pretesting appears to provide little benefit for learning conceptual information. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The use of phrase-level prosodic information in lexical segmentation: evidence from word-spotting experiments in Korean.

PubMed

Kim, Sahyang; Cho, Taehong

2009-05-01

This study investigated the role of phrase-level prosodic boundary information in word segmentation in Korean with two word-spotting experiments. In experiment 1, it was found that intonational cues alone helped listeners with lexical segmentation. Listeners paid more attention to local intonational cues (...H#L...) across the prosodic boundary than the intonational information within a prosodic phrase. The results imply that intonation patterns with high frequency are used, though not exclusively, in lexical segmentation. In experiment 2, final lengthening was added to see how multiple prosodic cues influence lexical segmentation. The results showed that listeners did not necessarily benefit from the presence of both intonational and final lengthening cues: Their performance was improved only when intonational information contained infrequent tonal patterns for boundary marking, showing only partially cumulative effects of prosodic cues. When the intonational information was optimal (frequent) for boundary marking, however, poorer performance was observed with final lengthening. This is arguably because the phrase-initial segmental allophonic cues for the accentual phrase were not matched with the prosodic cues for the intonational phrase. It is proposed that the asymmetrical use of multiple cues was due to interaction between prosodic and segmental information that are computed in parallel in lexical segmentation.

Initial retrieval shields against retrieval-induced forgetting.

PubMed

Racsmány, Mihály; Keresztes, Attila

2015-01-01

Testing, as a form of retrieval, can enhance learning but it can also induce forgetting of related memories, a phenomenon known as retrieval-induced forgetting (RIF). In four experiments we explored whether selective retrieval and selective restudy of target memories induce forgetting of related memories with or without initial retrieval of the entire learning set. In Experiment 1, subjects studied category-exemplar associations, some of which were then either restudied or retrieved. RIF occurred on a delayed final test only when memories were retrieved and not when they were restudied. In Experiment 2, following the study phase of category-exemplar associations, subjects attempted to recall all category-exemplar associations, then they selectively retrieved or restudied some of the exemplars. We found that, despite the huge impact on practiced items, selective retrieval/restudy caused no decrease in final recall of related items. In Experiment 3, we replicated the main result of Experiment 2 by manipulating initial retrieval as a within-subject variable. In Experiment 4 we replicated the main results of the previous experiments with non-practiced (Nrp) baseline items. These findings suggest that initial retrieval of the learning set shields against the forgetting effect of later selective retrieval. Together, our results support the context shift theory of RIF.

Gay and Lesbian Spirituality: A Response to Donaldson.

ERIC Educational Resources Information Center

Barret, Bob; Barzan, Robert

1998-01-01

A final response to S. M. Donaldson's comments (1998) on the authors' article, "Spiritual Experiences of Gay Men and Lesbians." The original article focused on the experiences and spiritual issues of self-identified gay men and lesbians. (Author/MKA)

LTPP pavement maintenance materials : PCC partial-depth spall repair experiment, final report.

DOT National Transportation Integrated Search

1999-10-01

The Strategic Highway Research Program (SHRP) H-106 maintenance experiment and the Federal Highway Administration : (FHWA) Long-Term Monitoring (LTM) of Pavement Maintenance Materials Test Sites project studied the repair of partialdepth : spalls in ...

Building confidence for work as house officers: student experience in the final year of a new problem-based curriculum.

PubMed

Whitehouse, Carl R; O'Neill, Paul; Dornan, Tim

2002-08-01

Newly qualified doctors require an appropriate level of confidence for their new roles. Development of this confidence was a key objective in the final year of a new integrated course with an emphasis on student self-direction. There are 5 placements in the final year course. Students use a Learning Planner to help them choose suitable placements and objectives to serve their learning needs. Educational supervision focuses on helping students determine their objectives and assessing them against these. Course evaluation was by means of a questionnaire during final assessments. Cohorts of 310 and 316 students in successive years completed the evaluation. The interrelationship between variables was explored using logistic regression. 220/310 students in the 2000 cohort and 214/316 in the 2001 cohort agreed they felt confident with their prospective role as a pre-registration house officer (PRHO). Confidence was significantly associated with confidence in their clinical skills, belief in their ability to cope with uncertainty and feeling able to work as a team member. The experience of the 2 hospital placements and (in 2000 only) the elective was associated with increased confidence. In all placements helpful educational supervision and the achievement of the self-directed learning plan was associated with increased confidence as a potential doctor. Students perceive a relationship between learning experiences in the final year of a self-directed course and development of confidence for their future role. Whilst further elucidation of the nature of this relationship is required, this provides encouragement to curriculum planners to promote self-direction.

BESTNET: Binational English & Spanish Telecommunications Network. Final FIPSE Report.

ERIC Educational Resources Information Center

Arias, Armando A., Jr.; Bellman, Beryl L.

The final evaluation of BESTNET (the Binational English and Spanish Telecommunications Network) is described. Undertaken as a collaborative effort to experiment with new telecommunications media in distance education and to attract Hispanic students into the science and engineering fields, the project involved the development of a number of…

76 FR 12044 - Stainless Steel Bar From India: Preliminary Results of, and Partial Rescission of, the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-04

... Facor did not experience significant differences in sales process/marketing support, freight/ delivery... Department re-examined Venus Wire's corporate affiliation relationship with Precision Metals for the instant administrative review. Because this relationship is unchanged from the 2005-2006 Final Results, 2007-2008 Final...

A Predictive Study of Pre-Service Teachers and Success in Final Student Internship

ERIC Educational Resources Information Center

Ingle, Karen M.

2017-01-01

Student teaching provides the final pre-service clinical teaching experience of an initial teacher preparation program. Research that specifically studies the pre-service student teacher and predictive factors of student teaching is limited. Identifying predictive factors that contribute to the success of student interns' student teaching…

Final Evaluation for the Neighborhood Educational Cultural Centerette.

ERIC Educational Resources Information Center

Frost, Patricia

Contained in this report is the final evaluation for the Neighborhood Educational Cultural Centerette Project. Objectives of the research project were to: (1) investigate, experiment with, create, and evaluate methods of instruction curriculum, and materials; analyze pupil learning styles and teacher-teaching styles; and to provide staff growth…

Comparison-Bot: an Automated Preliminary-Final Report Comparison System.

PubMed

Kalaria, Amit D; Filice, Ross W

2016-06-01

Regular comparison of preliminary to final reports is a critical part of radiology resident and fellow education as prior research has documented substantial preliminary to final discrepancies. Unfortunately, there are many barriers to this comparison: high study volume; overnight rotations without an attending; the ability to finalize reports remotely; the subtle nature of many changes; and lack of easy access to the preliminary report after finalization. We developed a system that automatically compiles and emails a weekly summary of report differences for all residents and fellows. Trainees can also create a custom report using a date range of their choice and can view this data on a resident dashboard. Differences between preliminary and final reports are clearly highlighted with links to the associated study in Picture Archiving and Communication Systems (PACS) for efficient review and learning. Reports with more changes, particularly changes made in the impression, are highlighted to focus attention on those exams with substantive edits. Our system provides an easy way for trainees to review changes to preliminary reports with immediate access to the associated images, thereby improving their educational experience. Departmental surveys showed that our report difference summary is easy to understand and improves the educational experience of our trainees. Additionally, interesting descriptive statistics help us understand how reports are changed by trainee level, by attending, and by exam type. Finally, this system can be easily ported to other departments who have access to their Health Level 7 (HL7) data.

Partial Return Yoke for MICE Step IV and Final Step

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, Holger; Plate, Stephen; Berg, J.Scott

2015-06-01

This paper reports on the progress of the design and construction of a retro-fitted return yoke for the international Muon Ionization Cooling Experiment (MICE). MICE is a proof-of-principle experiment aiming to demonstrate ionization cooling experimentally. In earlier studies we outlined how a partial return yoke can be used to mitigate stray magnetic field in the experimental hall; we report on the progress of the construction of the partial return yoke for MICE Step IV. We also discuss an extension of the Partial Return Yoke for the final step of MICE; we show simulation results of the expected performance.

Partial return yoke for MICE step IV and final step

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, H.; Plate, S.; Berg, J. S.

2015-05-03

This paper reports on the progress of the design and construction of a retro-fitted return yoke for the international Muon Ionization Cooling Experiment (MICE). MICE is a proof-of-principle experiment aiming to demonstrate ionization cooling experimentally. In earlier studies we outlined how a partial return yoke can be used to mitigate stray magnetic field in the experimental hall; we report on the progress of the construction of the partial return yoke for MICE Step IV. We also discuss an extension of the Partial Return Yoke for the final step of MICE; we show simulation results of the expected performance.

[Claim and reality of selective contact options : experiences in finalizing selective contracts in urological care].

PubMed

Ex, P; Schroeder, A

2014-08-01

Selective contracts are an important component in addition to the total healthcare concept in order to introduce process-related innovations into the healthcare system. Since 2011 the Berufsverband der Deutschen Urologen (BDU, Professional Association of German Urologists) has held negotiations with individual health insurance companies and care providers in order to view selective contracts as collective contracts, not only as pilot projects but also as additional forms of care.This article illustrates the experiences of the BDU in the initiation and finalizing of selective contracts as well as existing weak points in the framework conditions.

Final Results from the Jefferson Lab Qweak Experiment

NASA Astrophysics Data System (ADS)

Smith, Gregory

2017-09-01

The Qweak collaboration has unblinded our final result. We briefly describe the e-> p elastic scattering experiment used to extract the asymmetries measured in the two distinct running periods which constituted the experiment. The precision obtained on the final combined asymmetry is +/- 9.3 ppb. Some of the backgrounds and corrections applied in the experiment will be explained and quantified. We then provide the results of several methods we have used to extract consistent values of the proton's weak charge QWp from our asymmetry measurements. We also present results for the strange and axial form factors obtained from a fit to existing parity-violating electron scattering data. In conjunction with existing atomic parity violation results on 133Cs we extract the vector weak quark couplings C1u and C1d. The latter are combined to obtain the neutron's weak charge. From the proton's weak charge we obtain a result for sin2θW at the energy scale of our experiment, a sensitive SM test of the running of sin2θW . We also show the mass reach for new beyond-the-Standard-Model physics obtained from our determination of the proton's weak charge and its uncertainty, and discuss sensitivity to specific models. This work was supported by the U.S. Department of Energy, Office of Science, under Contract DE-AC05-06OR23177, the Natural Sciences and Engineering Research Council of Canada (NSERC), and the National Science Foundation (NSF).

How Long is Short?: Principles and Practice in the Delivery of Work Experience in Geography.

ERIC Educational Resources Information Center

Shepherd, Ifan D. H.

1998-01-01

Describes the development and implementation of the "short and thin" model of work experience at the Middlesex University geography program. The work experience program operates during the student's final year and is both "short" (10 weeks) and "thin" (one day a week). Outline the advantages and drawbacks of this…

Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

NASA Astrophysics Data System (ADS)

Katz, Daniel S.; Niemeyer, Kyle E.; Gesing, Sandra; Hwang, Lorraine; Bangerth, Wolfgang; Hettrick, Simon; Idaszak, Ray; Salac, Jean; Hong, Neil Chue; Núñez-Corrales, Santiago; Allen, Alice; Geiger, R. Stuart; Miller, Jonah; Chen, Emily; Dubey, Anshu; Lago, Patricia

This article summarizes motivations, organization, and activities of the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4). The WSSSPE series promotes sustainable research software by positively impacting principles and best practices, careers, learning, and credit. This article discusses the code of conduct; the mission and vision statements that were drafted at the workshop and finalized shortly after it; the keynote and idea papers, position papers, experience papers, demos, and lightning talks presented during the workshop; and a panel discussion on best practices. The main part of the article discusses the set of working groups that formed during the meeting, along with contact information for readers who may want to join a group. Finally, it discusses a survey of the workshop attendees.

Human Factors Experiments for Data Link : Final Report

DOT National Transportation Integrated Search

1975-11-01

This report describes the results of a series of experiments to evaluate cockpit Input/Output devices for Data Link as Phase I of a larger project to explore all facets of the digital transmission of air traffic control information. Following prelimi...

Thermal Control Surfaces Experiment

NASA Technical Reports Server (NTRS)

Wilkes, D. R.

1999-01-01

This report is the final experiment report for the TCSE and summarizes many years of hardware development and analyses. Also included are analyses presented in a number of TCSE papers that were prepared and given at scientific conferences including three LDEF Post-Retrieval Symposiums.

Experience with a second language affects the use of fundamental frequency in speech segmentation

PubMed Central

Broersma, Mirjam; Cho, Taehong; Kim, Sahyang; Martínez-García, Maria Teresa; Connell, Katrina

2017-01-01

This study investigates whether listeners’ experience with a second language learned later in life affects their use of fundamental frequency (F0) as a cue to word boundaries in the segmentation of an artificial language (AL), particularly when the cues to word boundaries conflict between the first language (L1) and second language (L2). F0 signals phrase-final (and thus word-final) boundaries in French but word-initial boundaries in English. Participants were functionally monolingual French listeners, functionally monolingual English listeners, bilingual L1-English L2-French listeners, and bilingual L1-French L2-English listeners. They completed the AL-segmentation task with F0 signaling word-final boundaries or without prosodic cues to word boundaries (monolingual groups only). After listening to the AL, participants completed a forced-choice word-identification task in which the foils were either non-words or part-words. The results show that the monolingual French listeners, but not the monolingual English listeners, performed better in the presence of F0 cues than in the absence of such cues. Moreover, bilingual status modulated listeners’ use of F0 cues to word-final boundaries, with bilingual French listeners performing less accurately than monolingual French listeners on both word types but with bilingual English listeners performing more accurately than monolingual English listeners on non-words. These findings not only confirm that speech segmentation is modulated by the L1, but also newly demonstrate that listeners’ experience with the L2 (French or English) affects their use of F0 cues in speech segmentation. This suggests that listeners’ use of prosodic cues to word boundaries is adaptive and non-selective, and can change as a function of language experience. PMID:28738093

Sub-Project 7 of Wisconsin 553, Part F, EPDA--Industry/Exchange Program: Final Report.

ERIC Educational Resources Information Center

Wisconsin Univ. - Stout, Menomonie. Center for Vocational, Technical and Adult Education.

The final report describes a study to develop a statewide teacher/industry exchange program in Wisconsin that would provide vocational-technical instructors with occupational experience opportunities. Three plans for implementing the program were developed: (A) swapping the positions of a business or industrial person with that of a vocational…

Reflectivity and Teaching Performance of Novice Teachers: Three Years of Investigation

ERIC Educational Resources Information Center

Pultorak, Edward; Barnes, Debbie

2009-01-01

The purpose of this 3-year investigation was to determine if a relationship exists between teacher reflectivity and the classroom performance of novice teachers when final evaluations are aligned with national standards. This study included 98 novice teachers enrolled in their final field-based teaching experience. Participants reflected over two…

Two Arts. Revision and What It Leaves behind

ERIC Educational Resources Information Center

Booten, Kyle

2012-01-01

Inspired by an experience of teaching the drafts of Elizabeth Bishop's "One Art", this article rereads the drafts as far more than imperfect precursors to the final poem. The drafts have their own prosodic features and poetic logic, one that values and enacts a vertiginous dilation of thought, expression and memory. The final version of…

Applied and Transformed Understanding in Introductory Psychology: Analysis of a Final Essay Assignment

ERIC Educational Resources Information Center

Clark, Kevin M.

2010-01-01

This paper describes a case study of the impact of the introductory psychology course on students' understanding of their life experiences and course-related ideas. Student responses to a final essay assignment were analyzed to construct composites for areas of applied and transformed understanding. Results are important for psychology teachers…

Effects of stocking density on growth performance, carcass traits, and foot pad lesions of White Pekin ducks.

PubMed

Xie, M; Jiang, Y; Tang, J; Wen, Z G; Huang, W; Hou, S S

2014-07-01

Two experiments were conducted to study the effects of stocking density on growth performance, carcass yield, and foot pad lesions of White Pekin ducks from hatch to 14 d of age (experiment 1) and from 14 to 42 d of age (experiment 2), respectively. All ducks were reared in raised plastic wire-floor pens with a pen size of 30 m(2), and males and females were mixed at a ratio of 1:1 in each pen of both experiments. In experiment 1, a total of 10,200 ducks that were 1 d old were allotted to 20 pens according to the stocking densities of 13, 15, 17, 19, and 21 birds/m(2) (or 8.4, 9.7, 10.9, 11.9, and 13.0 kg of actually achieved BW/m(2)), respectively, with 4 replicates per treatment. In experiment 2, a total of 3,150 ducks that were 14 d old were allotted to 15 pens according to the stocking densities of 5, 6, 7, 8, and 9 birds/m(2) (or 17.0, 20.3, 23.6, 26.9, and 29.9 kg of actually achieved BW/m(2)), respectively, with 3 replicates per treatment. The stocking density had significant effects on final BW and weight gain of starter and growing ducks (P < 0.05), but not on feed/gain and mortality in both periods (P > 0.05). The final BW and weight gain of starter and growing ducks all decreased with increasing density (P < 0.05). Final BW and weight gain of starter ducks were reduced significantly as stocking density increased from 17 to 21 birds/m(2) (P < 0.05). In addition, final BW and weight gain of growing ducks decreased significantly when stocking density was 9 birds/m(2) (P < 0.05). On the other hand, increasing stocking density did not markedly influence the carcass, breast meat, leg meat, abdominal fat, and foot pad lesions of growing ducks (P > 0.05). © 2014 Poultry Science Association Inc.

The effects of initial testing on false recall and false recognition in the social contagion of memory paradigm.

PubMed

Huff, Mark J; Davis, Sara D; Meade, Michelle L

2013-08-01

In three experiments, participants studied photographs of common household scenes. Following study, participants completed a category-cued recall test without feedback (Exps. 1 and 3), a category-cued recall test with feedback (Exp. 2), or a filler task (no-test condition). Participants then viewed recall tests from fictitious previous participants that contained erroneous items presented either one or four times, and then completed final recall and source recognition tests. The participants in all conditions reported incorrect items during final testing (a social contagion effect), and across experiments, initial testing had no impact on false recall of erroneous items. However, on the final source-monitoring recognition test, initial testing had a protective effect against false source recognition: Participants who were initially tested with and without feedback on category-cued initial tests attributed fewer incorrect items to the original event on the final source-monitoring recognition test than did participants who were not initially tested. These data demonstrate that initial testing may protect individuals' memories from erroneous suggestions.

Sun and Shade Leaves: Some Field Investigations.

ERIC Educational Resources Information Center

Tomley, David

1983-01-01

Several simple experiments illustrating how the light regime affects the final form of dog's mercury (Mercurialis perennis) are provided. These experiments, which can also be done with other plants, focus on differences in the anatomy, morphology, and physiology of sun and shade leaves. (JN)

Teaching the EPR Paradox at High School?

ERIC Educational Resources Information Center

Pospiech, Gesche

1999-01-01

Argues the importance of students at university and in the final years of high school gaining an appreciation of the principles of quantum mechanics. Presents the EPR gedanken experiment (thought experiment) as a method of teaching the principles of quantum mechanics. (Author/CCM)

Final results of the PICASSO dark matter search experiment

NASA Astrophysics Data System (ADS)

Behnke, E.; Besnier, M.; Bhattacharjee, P.; Dai, X.; Das, M.; Davour, A.; Debris, F.; Dhungana, N.; Farine, J.; Fines-Neuschild, M.; Gagnebin, S.; Giroux, G.; Grace, E.; Jackson, C. M.; Kamaha, A.; Krauss, C. B.; Lafrenière, M.; Laurin, M.; Lawson, I.; Lessard, L.; Levine, I.; Marlisov, D.; Martin, J.-P.; Mitra, P.; Noble, A. J.; Plante, A.; Podviyanuk, R.; Pospisil, S.; Scallon, O.; Seth, S.; Starinski, N.; Stekl, I.; Wichoski, U.; Zacek, V.

2017-04-01

The PICASSO dark matter search experiment operated an array of 32 superheated droplet detectors containing 3.0 kg of C4F10 and collected an exposure of 231.4 kgd at SNOLAB between March 2012 and January 2014. We report on the final results of this experiment which includes for the first time the complete data set and improved analysis techniques including acoustic localization to allow fiducialization and removal of higher activity regions within the detectors. No signal consistent with dark matter was observed. We set limits for spin-dependent interactions on protons of σpSD = 1.32 × 10-2 pb (90% C.L.) at a WIMP mass of 20 GeV/c2. In the spin-independent sector we exclude cross sections larger than σpSI = 4.86 × 10-5 pb (90% C.L.) in the region around 7 GeV/c2. The pioneering efforts of the PICASSO experiment have paved the way forward for a next generation detector incorporating much of this technology and experience into larger mass bubble chambers.

Novel pre-alloyed powder processing of modified alnico 8: Correlation of microstructure and magnetic properties

DOE PAGES

Anderson, I. E.; Kassen, A. G.; White, E. M. H.; ...

2015-04-13

Progress is reviewed on development of an improved near-final bulk magnet fabrication process for alnico 8, as a non-rare earth permanent magnet with promise for sufficient energy density and coercivity for electric drive motors. This study showed that alnico bulk magnets in near-final shape can be made by simple compression molding from spherical high purity gas atomized pre-alloyed powder. Dwell time at peak sintering temperature (1250°C) greatly affected grain size of the resulting magnet alloys. This microstructure transformation was demonstrated to be useful for gaining partially aligned magnetic properties and boosting energy product. Furthermore, while a route to increased coercivitymore » was not identified by these experiments, manufacturability of bulk alnico magnet alloys in near-final shapes was demonstrated, permitting further processing and alloy modification experiments that can target higher coercivity and better control of grain anisotropy during grain growth.« less

The Development of a Pediatric Inpatient Experience of Care Measure: Child HCAHPS®

PubMed Central

Toomey, Sara L.; Zaslavsky, Alan M.; Elliott, Marc N.; Gallagher, Patricia M.; Fowler, Floyd J.; Klein, David J.; Shulman, Shanna; Ratner, Jessica; McGovern, Caitriona; LeBlanc, Jessica L.; Schuster, Mark A.

2016-01-01

CMS uses Adult HCAHPS® scores for public reporting and pay-for-performance for most U.S. hospitals, but no publicly available standardized survey of inpatient experience of care exists for pediatrics. To fill the gap, CMS/AHRQ commissioned the development of the Consumer Assessment of Healthcare Providers and Systems Hospital Survey – Child Version (Child HCAHPS), a survey of parents/guardians of pediatric patients (<18 years old) who were recently hospitalized. This Special Article describes the development of Child HCAHPS, which included an extensive review of the literature and quality measures, expert interviews, focus groups, cognitive testing, pilot testing of the draft survey, a national field test with 69 hospitals in 34 states, psychometric analysis, and end-user testing of the final survey. We conducted extensive validity and reliability testing to determine which items would be included in the final survey instrument and to develop composite measures. We analyzed national field test data from 17,727 surveys collected from 11/12-1/14 from parents of recently hospitalized children. The final Child HCAHPS instrument has 62 items, including 39 patient experience items, 10 screeners, 12 demographic/descriptive items, and 1 open-ended item. The 39 experience items are categorized based on testing into 18 composite and single-item measures. Our composite and single-item measures demonstrated good to excellent hospital-level reliability at 300 responses per hospital. Child HCAHPS was developed to be a publicly available standardized survey of pediatric inpatient experience of care. It can be used to benchmark pediatric inpatient experience across hospitals and assist in efforts to improve the quality of inpatient care. PMID:26195542

Wave-Sediment Interaction in Muddy Environments: A Field Experiment

DTIC Science & Technology

2009-01-01

Geosciences project includes a field experiment on the Atchafalaya shelf, Louisiana, in Years 1 and 2 (2007-2008) and a data analysis and modeling effort in... analysis procedures. During the major field experiment effort in 2008 (Year 2), a total of 5 tripods were deployed at locations fronting the Atchafalaya...experiment effort. This final year of the project (2009, Year 3) has been focused upon data analysis and preparation of publications. APPROACH

More than Relations between Self, Others and Nature: Outdoor Education and Aesthetic Experience

ERIC Educational Resources Information Center

Quay, John

2013-01-01

Self, others and nature (environment) have been suggested over numerous decades and in various places as a way of understanding experience in outdoor education. These three elements and the relations between them appear to cover it all. But is this really the final word on understanding experience? In this paper I explore two emphases within…

The Programme of Experiments in Intercultural Education from 1986 to 1991. Final Educational Evaluation.

ERIC Educational Resources Information Center

Perotti, Antonio; And Others

This document reports on a five year series of experiments in intercultural education. The main lessons emerging from the project are summarized under four headings: (1) the new frame of reference in analyzing the problem; (2) new concepts and new educational aims and content; (3) results and limitations of the experiments in relation to the new…

[Burdened into the job -- final-year students' empathy and burnout].

PubMed

Koehl-Hackert, Nadja; Schultz, Jobst-Hendrik; Nikendei, Christoph; Möltner, Andreas; Gedrose, Benjamin; van den Bussche, Hendrik; Jünger, Jana

2012-01-01

Empathy is a central element in daily patient care. The burnout syndrome seems to be a potential factor influencing physicians' empathic behavior negatively. In Germany up to 20 % of practicing physicians experience burnout. So far, there have been no studies measuring empathy and the degree of burnout among final-year medical students in Germany. The aim of the current study was to investigate final-year students' self-reported empathy, burnout and the association of job satisfaction and occupational self-efficacy with regard to potential gender differences. 127 medical students at the end of their final year (82 f, 45 m; 26.8 years of age) were surveyed using the Jefferson Scale of Physician Empathy (JSPE), the Maslach Burnout Inventory (MBI) and items addressing job satisfaction and occupational self-efficacy. The mean JSPE score of all final-year students was 113.25 ± 10.21 (20=lowest possible empathy score, 140=highest possible empathy score). Based on the three dimensions of burnout, the students fell in the moderate burnout category in all subscales of the MBI. There was an association between a lower empathy score and a higher burnout score. Also, the MBI correlated negatively with final-year students' job satisfaction and occupational self-efficacy. Despite high self-rated empathy scores, the experience of burnout symptoms in medical students may begin as early as their final year of studies, where higher levels of burnout are associated with lower self-rated empathy scores. The number of final-year medical students affected by clinically significant burnout (up to 20 %) was just as high as among practicing physicians. Female students were found to be particularly affected. Given the rising numbers of female graduates, this shows that urgent action is required. Copyright © 2012. Published by Elsevier GmbH.

Forward-Backward Asymmetry of Top Quark Pair Productionn at the Fermilab Tevatron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Ziqing

2015-12-01

This dissertation presents the final measurements of the forward-backward asymmetry (A FB) of top quark-antiquark pair events (t t -) at the Collider Detector at Fermilab (CDF) experiment. The t t - events are produced in proton{anti-proton collisions with a center of mass energy of 1:96 TeV during the Run II of the Fermilab Tevatron. The measurements are performed with the full CDF Run II data (9.1 fb -1) in the final state that contain two charged leptons (electrons or muons, the dilepton final state), and are designed to con rm or deny the evidence-level excess in the AFB measurementsmore » in the final state with a single lepton and hadronic jets (lepton+jets final state) as well as the excess in the preliminary measurements in the dilepton final state with the first half of the CDF Run II data. New measurements include the leptonic AFB (A l FB), the lepton-pair A FB (A ll FB) and the reconstructed top AFB (At t FB). Each are combined with the previous results from the lepton+jets final state measured at the CDF experiment. The inclusive A l FB, A ll FB, and At t FB measured in the dilepton final state are 0.072 ± 0.060, 0.076 ± 0.081, and 0.12 ± 0.13, to be compared with the Standard Model (SM) predictions of 0.038 ± 0.003, 0.048 ± 0.004, and 0.010 ± 0.006, respectively. The CDF combination of A l FB and At t FB are 0.090 +0:028 -0.026, and 0.160 ± 0.045, respectively. The overall results are consistent with the SM predictions.« less

Patient Protection and Affordable Care Act; annual eligibility redeterminations for exchange participation and insurance affordability programs; health insurance issuer standards under the Affordable Care Act, including standards related to exchanges. Final rule.

PubMed

2014-09-05

This final rule specifies additional options for annual eligibility redeterminations and renewal and re-enrollment notice requirements for qualified health plans offered through the Exchange, beginning with annual redeterminations for coverage for benefit year 2015. This final rule provides additional flexibility for Exchanges, including the ability to propose unique approaches that meet the specific needs of their state, while streamlining the consumer experience.

Constraints on the Transfer of Perceptual Learning in Accented Speech

PubMed Central

Eisner, Frank; Melinger, Alissa; Weber, Andrea

2013-01-01

The perception of speech sounds can be re-tuned through a mechanism of lexically driven perceptual learning after exposure to instances of atypical speech production. This study asked whether this re-tuning is sensitive to the position of the atypical sound within the word. We investigated perceptual learning using English voiced stop consonants, which are commonly devoiced in word-final position by Dutch learners of English. After exposure to a Dutch learner’s productions of devoiced stops in word-final position (but not in any other positions), British English (BE) listeners showed evidence of perceptual learning in a subsequent cross-modal priming task, where auditory primes with devoiced final stops (e.g., “seed”, pronounced [si:th]), facilitated recognition of visual targets with voiced final stops (e.g., SEED). In Experiment 1, this learning effect generalized to test pairs where the critical contrast was in word-initial position, e.g., auditory primes such as “town” facilitated recognition of visual targets like DOWN. Control listeners, who had not heard any stops by the speaker during exposure, showed no learning effects. The generalization to word-initial position did not occur when participants had also heard correctly voiced, word-initial stops during exposure (Experiment 2), and when the speaker was a native BE speaker who mimicked the word-final devoicing (Experiment 3). The readiness of the perceptual system to generalize a previously learned adjustment to other positions within the word thus appears to be modulated by distributional properties of the speech input, as well as by the perceived sociophonetic characteristics of the speaker. The results suggest that the transfer of pre-lexical perceptual adjustments that occur through lexically driven learning can be affected by a combination of acoustic, phonological, and sociophonetic factors. PMID:23554598

Interpolated testing influences focused attention and improves integration of information during a video-recorded lecture.

PubMed

Jing, Helen G; Szpunar, Karl K; Schacter, Daniel L

2016-09-01

Although learning through a computer interface has become increasingly common, little is known about how to best structure video-recorded lectures to optimize learning. In 2 experiments, we examine changes in focused attention and the ability for students to integrate knowledge learned during a 40-min video-recorded lecture. In Experiment 1, we demonstrate that interpolating a lecture with memory tests (tested group), compared to studying the lecture material for the same amount of time (restudy group), improves overall learning and boosts integration of related information learned both within individual lecture segments and across the entire lecture. Although mind wandering rates between the tested and restudy groups did not differ, mind wandering was more detrimental for final test performance in the restudy group than in the tested group. In Experiment 2, we replicate the findings of Experiment 1, and additionally show that interpolated tests influence the types of thoughts that participants report during the lecture. While the tested group reported more lecture-related thoughts, the restudy group reported more lecture-unrelated thoughts; furthermore, lecture-related thoughts were positively related to final test performance, whereas lecture-unrelated thoughts were negatively related to final test performance. Implications for the use of interpolated testing in video-recorded lectures are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Carbon isotope effects associated with mixed-acid fermentation of saccharides by Clostridium papyrosolvens

NASA Astrophysics Data System (ADS)

Penning, Holger; Conrad, Ralf

2006-05-01

In anoxic environments, microbial fermentation is the first metabolic process in the path of organic matter degradation. Since little is known about carbon isotope fractionation during microbial fermentation, we studied mixed-acid fermentation of different saccharides (glucose, cellobiose, and cellulose) in Clostridium papyrosolvens. The bacterium was grown anaerobically in batch under different growth conditions, both in pure culture and in co-culture with Methanobacterium bryantii utilizing H 2/CO 2 or Methanospirillum hungatei utilizing both H 2/CO 2 and formate. Fermentation products were acetate, lactate, ethanol, formate, H 2, and CO 2 (and CH 4 in methanogenic co-culture), with acetate becoming dominant at low H 2 partial pressures. After complete conversion of the saccharides, acetate was 13C-enriched ( αsacc/ac = 0.991-0.997), whereas lactate ( αsacc/lac = 1.001-1.006), ethanol ( αsacc/etoh = 1.007-1.013), and formate ( αsacc/form = 1.007-1.011) were 13C-depleted. The total inorganic carbon produced was only slightly enriched in 13C, but was more enriched, when formate was produced in large amounts, as 12CO 2 was preferentially converted with H 2 to formate. During biomass formation, 12C was slightly preferred ( αsacc/biom ≈ 1.002). The observations in batch culture were confirmed in glucose-limited chemostat culture at growth rates of 0.02-0.15 h -1 at both low and high hydrogen partial pressures. Our experiments showed that the carbon flow at metabolic branch points in the fermentation path governed carbon isotope fractionation to the accumulated products. During production of pyruvate, C isotopes were not fractionated when using cellulose, but were fractionated to different extents depending on growth conditions when using cellobiose or glucose. At the first catabolic branch point (pyruvate), the produced lactate was depleted in 13C, whereas the alternative product acetyl-CoA was 13C enriched. At the second branch point (acetyl-CoA), the ethanol formed was 15.6-18.6‰ depleted in 13C compared to the alternative product acetate. At low hydrogen partial pressures, as normally observed under environmental conditions, fermentation of saccharides should mainly result in the production of acetate that is only slightly enriched in 13C (<3‰).

Mineral Magnetic Properties of Partially Oxidized Siderite

NASA Astrophysics Data System (ADS)

Dekkers, M. J.; Hanckmann, W. J. F.; Spassov, S.; Behrends, T.

2017-12-01

Siderite (FeCO3) is an important mineral in iron redox cycling in the subsurface. It is often characterized geochemically by means of various sequential extraction schemes. However, a mineralogical siderite determination remains rather tedious, particularly when dealing with trace amounts and very fine particles, often the rule in soils and sediments. Here we explore the suitability of the very sensitive magnetic methods to this end, exploiting siderite's magnetic properties at low temperature. The basic magnetic properties of siderite are surprisingly poorly characterized. To contribute to this issue, we have synthesized siderite with varying amounts of ferric iron in a chemostat, next to the magnetic characterization of several siderites from mineral collections. By slowly adding ferrous iron perchlorate to a carbonate solution the synthesis could be tweaked in order to deliver products as crystalline as possible. Synthesis products were verified with XRD; at pH below 7 siderite was the dominant phase, at higher pH the mineral chukanovite (Fe2(OH)2CO3) was found. The degree of oxidation was measured wet-chemically with the ferrozine method. Samples appeared to be oxidized between 1 and 80%, most samples between 1 and 6%. The sequence of low temperature magnetic measurements (on an MPMS3 system) included 1) cooling in a field of 15 mT to 5 K, 2) warming of a 5 T IRM given at 5 K in zero field to 300 K, 3) cooling in a field of 5 T to 5 K, and 4) warming of the field-cooled 5 T IRM in zero field to 300 K. For mineral collection siderite also hysteresis loops were determined at several temperatures to determine the exchange bias field. Conform literature data siderite was found to have a magnetic ordering temperature of 38 K. Oxidation appears to smear out the remanence warming curves while also shifting the ordering temperature upward. Specific magnetic moments were found to vary distinctly, being both lower and higher than reference values. We relate this tentatively to grain size effects that play up since siderite is an antiferromagnet and far from saturation in a 5 T field. Standard addition experiments indicated that one per mil siderite can be traced rock-magnetically, enabling a check on sequential extraction schemes designed to allocate iron to several redox-sensitive pools in natural samples.

[MODIS Investigation

NASA Technical Reports Server (NTRS)

Abbott, Mark R.

1998-01-01

The objective of the last six months were: (1) Continue analysis of Hawaii Ocean Time-series (HOT) bio-optical mooring data, and Southern Ocean bio-optical drifter data; (2) Complete development of documentation of MOCEAN algorithms and software for use by MOCEAN team and GLI team; (3) Deploy instrumentation during JGOFS cruises in the Southern Ocean; (4) Participate in test cruise for Fast Repetition Rate (FRR) fluorometer; (5) Continue chemostat experiments on the relationship of fluorescence quantum yield to environmental factors; and (6) Continue to develop and expand browser-based information system for in situ bio-optical data. We are continuing to analyze bio-optical data collected at the Hawaii Ocean Time Series mooring as well as data from bio-optical drifters that were deployed in the Southern Ocean. A draft manuscript has now been prepared and is being revised. A second manuscript is also in preparation that explores the vector wind fields derived from NSCAT measurements. The HOT bio-optical mooring was recovered in December 1997. After retrieving the data, the sensor package was serviced and redeployed. We have begun preliminary analysis of these data, but we have only had the data for 3 weeks. However, all of the data were recovered, and there were no obvious anomalies. We will add second sensor package to the mooring when it is serviced next spring. In addition, Ricardo Letelier is funded as part of the SeaWiFS calibration/validation effort (through a subcontract from the University of Hawaii, Dr. John Porter), and he will be collecting bio-optical and fluorescence data as part of the HOT activity. This will provide additional in situ measurements for MODIS validation. As noted in the previous quarterly report, we have been analyzing data from three bio-optical drifters that were deployed in the Southern Ocean in September 1996. We presented results on chlorophyll and drifter speed. For the 1998 Ocean Sciences meeting, a paper will be presented on this data set, focusing on the diel variations in fluorescence quantum yield. Briefly, there are systematic patterns in the apparent quantum yield of fluorescence (defined as the slope of the line relating fluorescence/chlorophyll and incoming solar radiation). These systematic variations appear to be related to changes in the circulation of the Antarctic Polar Front which force nutrients into the upper ocean. A more complete analysis will be provided in the next Quarterly report.

An Appraisal of a New Undergraduate Biochemistry Research Project.

ERIC Educational Resources Information Center

Adamson, Ishola

1980-01-01

Described is the first part of a two-term project involving final-year students in biochemistry. Listed are the required experiments compiled to test students' abilities to search biochemical literature, extract experiments from journals and carry them out, generate data, and interpret results. (CS)

IER-297 CED-2: Final Design for Thermal/Epithermal eXperiments with Jemima Plates with Polyethylene and Hafnium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, A. J.; Percher, C. M.; Zywiec, W. J.

This report presents the final design (CED-2) for IER-297, and focuses on 15 critical configurations using highly enriched uranium (HEU) Jemima plates moderated by polyethylene with and without hafnium diluent. The goal of the U.S. Nuclear Criticality Safety Program’s Thermal/Epithermal eXperiments (TEX) is to design and conduct new critical experiments to address high priority nuclear data needs from the nuclear criticality safety and nuclear data communities, with special emphasis on intermediate energy (0.625 eV – 100 keV) assemblies that can be easily modified to include various high priority diluent materials. The TEX (IER 184) CED-1 Report [1], completed in 2012,more » demonstrated the feasibility of meeting the TEX goals with two existing NCSP fissile assets, plutonium Zero Power Physics Reactor (ZPPR) plates and highly enriched uranium (HEU) Jemima plates. The first set of TEX experiments will focus on using the plutonium ZPPR plates with polyethylene moderator and tantalum diluents.« less

Retrieval attempts enhance learning regardless of time spent trying to retrieve.

PubMed

Vaughn, Kalif E; Hausman, Hannah; Kornell, Nate

2017-03-01

Attempting to retrieve information from memory is an engaging cognitive activity. We predicted that people would learn more when they had spent more time attempting to retrieve. In experiments 1a and 1b, participants were shown trivia questions for 0, 5, 10, or 30 seconds and then the answer was revealed. They took a final test immediately or after 48 hours. Retrieval enhanced learning, but the length of the retrieval attempt had no effect (i.e., final test performance was equivalent in the 5-, 10-, and 30-second conditions and worse in the 0-second condition). During the initial retrieval attempt, more time did increase recall, suggesting that participants continued to engage in productive retrieval activities when given more time. Showing the answer for longer (7 versus 2 seconds) increased learning in Experiments 2a and 2b. Experiment 3 examined the effect of retrieval success and Experiment 4 replicated the results using different materials. These results have direct implications for current theories of retrieval.

Partial polarization: a comprehensive student exercise

NASA Astrophysics Data System (ADS)

Topasna, Gregory A.; Topasna, Daniela M.

2015-10-01

We present a comprehensive student exercise in partial polarization. Students are first introduced to the concept of partial polarization using Fresnel Equations. Next, MATHCAD is used to compute and graph the reflectance for dielectrics materials. The students then design and construct a simple, easy to use collimated light source for their experiment, which is performed on an optical breadboard using optical components typically found in an optics lab above the introductory level. The students obtain reflection data that is compared with their model by a nonlinear least square fit using EXCEL. Sources of error and uncertainty are discussed and students present a final written report. In this one exercise students learn how an experiment is constructed "from the ground up". They gain practical experience on data modeling and analysis, working with optical equipment, machining and construction, and preparing a final presentation.

Initial retrieval shields against retrieval-induced forgetting

PubMed Central

Racsmány, Mihály; Keresztes, Attila

2015-01-01

Testing, as a form of retrieval, can enhance learning but it can also induce forgetting of related memories, a phenomenon known as retrieval-induced forgetting (RIF). In four experiments we explored whether selective retrieval and selective restudy of target memories induce forgetting of related memories with or without initial retrieval of the entire learning set. In Experiment 1, subjects studied category-exemplar associations, some of which were then either restudied or retrieved. RIF occurred on a delayed final test only when memories were retrieved and not when they were restudied. In Experiment 2, following the study phase of category-exemplar associations, subjects attempted to recall all category-exemplar associations, then they selectively retrieved or restudied some of the exemplars. We found that, despite the huge impact on practiced items, selective retrieval/restudy caused no decrease in final recall of related items. In Experiment 3, we replicated the main result of Experiment 2 by manipulating initial retrieval as a within-subject variable. In Experiment 4 we replicated the main results of the previous experiments with non-practiced (Nrp) baseline items. These findings suggest that initial retrieval of the learning set shields against the forgetting effect of later selective retrieval. Together, our results support the context shift theory of RIF. PMID:26052293

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anastasi, A.; Basti, A.; Bedeschi, F.

We report the test of many of the key elements of the laser-based calibration system for muon g - 2 experiment E989 at Fermilab. The test was performed at the Laboratori Nazionali di Frascati's Beam Test Facility using a 450 MeV electron beam impinging on a small subset of the final g - 2 lead-fluoride crystal calorimeter system. The calibration system was configured as planned for the E989 experiment and uses the same type of laser and most of the final optical elements. We show results regarding the calorimeter's response calibration, the maximum equivalent electron energy which can be providedmore » by the laser and the stability of the calibration system components.« less

Federal employees health benefits acquisition regulation: large provider agreements, subcontracts, and miscellaneous changes. Final rule.

PubMed

2005-06-01

The Office of Personnel Management (OPM) is issuing this final regulation to amend the Federal Employees Health Benefits Acquisition Regulation (FEHBAR). It establishes requirements, including audit, for Federal Employees Health Benefits Program (FEHB) experience-rated carriers' Large Provider Agreements. It also modifies the dollar threshold for review of carriers' subcontract agreements; revises the definitions of Cost or Pricing Data and Experience-rate to reflect mental health parity requirements; updates the contract records retention requirement; updates the FEHB Clause Matrix; and conforms subpart and paragraph references to Federal Acquisition Regulation (FAR) revisions made since we last updated the FEHBAR.

Arts, literature and reflective writing as educational strategies to promote narrative reasoning capabilities among physiotherapy students.

PubMed

Caeiro, Carmen; Cruz, Eduardo Brazete; Pereira, Carla Mendes

2014-11-01

The use of arts, literature and reflective writing has becoming increasingly popular in health professionals education. However, research examining its contribution as an educational strategy to promote narrative reasoning capabilities is limited, particularly from the students' perspective. This study aimed to explore the final year physiotherapy students' perspectives about the contribution of arts, literature and reflective writing in facilitating narrative reasoning capabilities. Three focus group meetings using a semi-structured interview schedule were carried out to collect data. Focus group sessions were audiotaped and transcribed verbatim. Interpretative phenomenological analysis was used to conduct the study and analyze the transcripts. Three themes emerged: (1) developmental understanding of the patients' experiences; (2) developmental understanding about the self; and (3) embedding reflection in clinical practice. Students emphasized an increasing capability to be sensitive and vicariously experience the patient's experience. Through reflective writing, students reported they became more capable of thinking critically about their practice and learning needs for continuous professional development. Finally, students highlighted the contribution of these strategies in making reflection part of their practice. Final year physiotherapy students reported enhanced skills of narrative reasoning. The findings support the inclusion of these strategies within the undergraduate physiotherapy curricula.

Difficulties Encountered by Final-Year Male Nursing Students in Their Internship Programmes

PubMed Central

Al-Momani, Mohammed Mahmoud

2017-01-01

Background The cultural norms of the Kingdom of Saudi Arabia do not encourage men to choose nursing as a career. Understanding male nursing students’ experiences of their clinical exposure to the nursing profession throughout their internship might increase their retention. This study explored the experiences of final-year male nursing students as they transitioned to the role of registered nurse. Methods A qualitative descriptive research design with an inductive content-analysis approach was used. The experiences of 22 final-year male nursing students from three public hospitals in a major city of Saudi Arabia were explored. The data were collected using focus-group interviews and documentary analysis in March 2015 and May 2015. Results Content analysis revealed three major themes: the societal and cultural image of male nurses, male students’ engagement in nursing practice, and restructuring the internship programmes’ policies to suit male students’ needs. Conclusion The findings reveal issues that mainly stem from negative social views of nursing as a male profession. Considering the students’ social and cultural needs during their internship programme will facilitate their transition into the role of registered nurse and their retention in the nursing profession. PMID:28951687

Participants' Perceptions of Their Outward Bound Final Expedition and the Relationship to Instructor Supervisory Position

ERIC Educational Resources Information Center

Bobilya, Andrew J.; Kalisch, Kenneth R.; Daniel, Brad

2014-01-01

The purpose of this mixed-method study was to understand participants' perceptions of their Outward Bound Final Expedition experience and more specifically the relationship between the instructor supervisory position and participant's perception of learning. A sample of 331 students consented to participate and completed a survey at the conclusion…

Ten Years of Using Presentations at a Student Conference as a Final Assessment

ERIC Educational Resources Information Center

Lund, Nick

2013-01-01

The final assessment for all psychology courses in the department of interdisciplinary studies, MMU Cheshire programmes, in the past 10 years has been a presentation of project work at an undergraduate conference. It is argued that this acts as an "authentic" assessment method which helps prepare students for future experiences. Alumni…

Microencapsulation of Drugs in the Microgravity Environment of the United States Space Shuttle - Follow-On Experiments

DTIC Science & Technology

1996-10-01

TITLE: Microencapsulation of Drugs in the Microgravity Environment of the United States Space Shuttle - Follow-On Experiments PRINCIPAL INVESTIGATOR...REPORT DATE 3. REPORT TYPE AND DATES COVERED October 1996 Final (4 May 92 - 3 Jul 96) 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Microencapsulation of...call the Microencapsulation in Space (MIS-B) experiment. The MIS-B experiment flew on Space Shuttle Discovery -- Mission STS-70. Before launch, NASA

Undergraduates' perceptions of the value of practical inhalation sedation experience in a UK dental school.

PubMed

Walley, S; Albadri, S

2015-10-01

This was to establish the level and reported value of paediatric IHS experience from the perspective of final year undergraduates and to evaluate whether those students with more experience expressed feeling better-prepared for future practice and more likely to undertake further postgraduate education in IHS. All final year students were invited to complete an anonymous questionnaire designed to elicit undergraduate perceptions of IHS using visual analogue scales and free-text questions. A response rate of 77 % was achieved. Results revealed that only 21 % of participants reported acting as operator sedationist in ten or more IHS cases. Thus, the majority of undergraduates' did not meet the recommended quantity of practical IHS experiences, as outlined by the British Dental Sedation Teachers Group. In general, students felt on the value of IHS in the management of anxious children and expressed a desire to undertake further postgraduate education in conscious sedation. However, those students with more experience of practical IHS expressed feeling better able to describe the IHS experience with patients and parents, and were more satisfied with the quality of teaching. Furthermore free-text comments revealed that, regardless of experience, students wished to gain more experience of the practical administration of IHS. There is a need to increase the provision of IHS training within an undergraduate curriculum, in addition to improving the accessibility of postgraduate sedation courses.

Alaska Education Experiment. Final Report. Volume I.

ERIC Educational Resources Information Center

Alaska Governor's Office of Telecommunications, Juneau.

Alaska is a state of geographic and cultural extremes. In order to improve the standard of health and to provide broader educational opportunity, especially in rural communities, the ATS-6 communications satellite has been used to compensate for remoteness and transportation difficulties. The Health/Education Telecommunications Experiment has…

San Antonio Experience Based Career Education Demonstration Project. Final Narrative Performance Report, September 15, 1976-August 31, 1979.

ERIC Educational Resources Information Center

Lafferty, Bill R.

The San Antonio Experience-Based Career Education (EBCE) project was evaluated by a third party for its three years of operation. The project was designed to assist youth in making a successful transition to adulthood through community-based and learning center experiences, and was implemented by the Harlandale and San Antonio school districts.…

A Study of Culturally Deprived Children in Kindergarten and Grade I Following a Nine-Month Nursery Experience. Final Report.

ERIC Educational Resources Information Center

Zigler, Edward F.

This follow-up study compares the social adjustment and academic performance of low-income kindergarten and first-grade children who participated in a 9-month Head Start-type nursery school experience with that of kindergarten and first-grade children from the same social background who had not had the nursery school experience. Children were…

The Problem of Representation and Experience in Quantum Mechanics

NASA Astrophysics Data System (ADS)

Ronde, Christian De

2014-03-01

In this paper we discuss the problem of representation and experience in quantum mechanics. We analyze the importance of metaphysics in physical thought and its relation to empiricism and analytic philosophy. We argue against both instrumentalism and scientific realism and claim that both perspectives tend to bypass the problem of representation and justify a "common sense" type experience. Finally, we present our expressionist conception of physics.

A Comparative Analysis of the Influence of Surface Mining on Hydrological and Geochemical Response of Selected Headwater Streams in the Elk Valley, British Columbia, Canada.

NASA Astrophysics Data System (ADS)

Carey, S. K.; Shatilla, N. J.; Szmudrowska, B.; Rastelli, J.; Wellen, C.

2014-12-01

Surface mining is a common method of accessing coal. Blasting of overburden rock allows access to mineable ore. In high-elevation environments, the removed overburden rock is deposited in adjacent valleys as waste rock spoils. As part of a multi-year R&D program examining the influence of surface mining on watershed hydrological and water quality responses in the Elk Valley, British Columbia, this study reports on how surface mining affects streamflow hydrological and geochemical response at four reference and four mine-influenced catchments. The hydrology of this environment is dominated by snowmelt and steep topographic gradients. Flows were attenuated in mine-influenced catchments, with spring freshet delayed and more muted responses to precipitation events observed. Dissolved ions were an order of magnitude greater in mine-influenced streams, with more dilution-based responses to flows compared with chemostatic behavior observed in reference streams. Stable isotope signatures in stream water suggested that in both mine-influenced and reference watersheds, stream water was derived from well mixed groundwater as annual variability of stream isotope signatures was dampened compared with precipitation signatures. However, deflection of stream isotopes in response to precipitation were more apparent in reference watersheds. As a group, mine influenced catchments had a heavier isotope signature than reference watersheds, suggesting an enhanced influence of rainfall on recharge. Transit time distributions indicate existing waste rock spoils increase the average time water takes to move through the catchment.

The linkage between nutrient supply, intracellular enzyme abundances and bacterial growth: New evidences from the central carbon metabolism of Corynebacterium glutamicum.

PubMed

Noack, Stephan; Voges, Raphael; Gätgens, Jochem; Wiechert, Wolfgang

2017-09-20

Corynebacterium glutamicum serves as important production host for small molecular compounds that are derived from precursor molecules of the central carbon metabolism. It is therefore a well-studied model organism of industrial biotechnology. However, a deeper understanding of the regulatory principles underlying the synthesis of central metabolic enzymes under different environmental conditions as well as its impact on cell growth is still missing. We studied enzyme abundances in C. glutamicum in response to growth on: (i) one limiting carbon source by sampling chemostat and fed-batch cultivations and (ii) changing carbon sources provided in excess by sampling batch cultivations. The targeted quantification of 20 central metabolic enzymes by isotope dilution mass spectrometry revealed that cells maintain stable enzyme concentrations when grown on d-glucose as single carbon and energy source and, most importantly, independent of its availability. By contrast, switching from d-glucose to d-fructose, d-mannose, d-arabitol, acetate, l-lactate or l-glutamate results in highly specific enzyme regulation patterns that can partly be explained by the activity of known transcriptional regulators. Based on these experimental results we propose a simple framework for modeling cell population growth as a nested function of nutrient supply and intracellular enzyme abundances. In summary, our study extends the basis for the formulation of predictive mechanistic models of bacterial growth, applicable in industrial bioprocess development. Copyright © 2017 Elsevier B.V. All rights reserved.

Competition between a nonallelopathic phytoplankton and an allelopathic phytoplankton species under predation.

PubMed

Kengwoung-Keumo, Jean-Jacques

2016-08-01

We propose a model of two-species competition in the chemostat for a single growth-limiting, nonreproducing resource that extends that of Roy [38]. The response functions are specified to be Michaelis-Menten, and there is no predation in Roy's work. Our model generalizes Roy's model to general uptake functions. The competition is exploitative so that species compete by decreasing the common pool of resources. The model also allows allelopathic effects of one toxin-producing species, both on itself (autotoxicity) and on its nontoxic competitor (phytotoxicity). We show that a stable coexistence equilibrium exists as long as (a) there are allelopathic effects and (b) the input nutrient concentration is above a critical value. The model is reconsidered under instantaneous nutrient recycling. We further extend this work to include a zooplankton species as a fourth interacting component to study the impact of predation on the ecosystem. The zooplankton species is allowed to feed only on the two phytoplankton species which are its perfectly substitutable resources. Each of the models is analyzed for boundedness, equilibria, stability, and uniform persistence (or permanence). Each model structure fits very well with some harmful algal bloom observations where the phytoplankton assemblage can be envisioned in two compartments, toxin producing and non-toxic. The Prymnesium parvum literature, where the suppressing effects of allelochemicals are quite pronounced, is a classic example. This work advances knowledge in an area of research becoming ever more important, which is understanding the functioning of allelopathy in food webs.

Decadal and seasonal trends of nutrient concentration and export from highly managed coastal catchments.

PubMed

Wan, Yongshan; Wan, Lei; Li, Yuncong; Doering, Peter

2017-05-15

Understanding anthropogenic and hydro-climatic influences on nutrient concentrations and export from highly managed catchments often necessitates trend detection using long-term monitoring data. This study analyzed the temporal trend (1979-2014) of total nitrogen (TN) and total phosphorus (TP) concentrations and export from four adjacent coastal basins in south Florida where land and water resources are highly managed through an intricate canal network. The method of integrated seasonal-trend decomposition using LOESS (LOcally weighted regrESSion) was employed for trend detection. The results indicated that long-term trends in TN and TP concentrations (increasing/decreasing) varied with basins and nutrient species, reflecting the influence of basin specific land and water management practices. These long-term trends were intervened by short-term highs driven by high rainfall and discharges and lows associated with regional droughts. Seasonal variations in TP were more apparent than for TN. Nutrient export exhibited a chemostatic behavior for TN from all the basins, largely due to the biogenic nature of organic N associated with the ubiquity of organic materials in the managed canal network. Varying degrees of chemodynamic export was present for TP, reflecting complex biogeochemical responses to the legacy of long-term fertilization, low soil P holding capacity, and intensive stormwater management. The anthropogenic and hydro-climatic influences on nutrient concentration and export behavior had great implications in nutrient loading abatement strategies for aquatic ecosystem restoration of the downstream receiving waterbody. Published by Elsevier Ltd.

Dynamics of Multiple lin Gene Expression in Sphingomonas paucimobilis B90A in Response to Different Hexachlorocyclohexane Isomers

PubMed Central

Suar, Mrutyunjay; van der Meer, Jan Roelof; Lawlor, Kirsten; Holliger, Christof; Lal, Rup

2004-01-01

Sphingomonas paucimobilis B90A is able to degrade the α-, β-, γ-, and δ-isomers of hexachlorocyclohexane (HCH). It contains the genes linA, linB, linC, linD, linE, and linR, which have been implicated in HCH degradation. In this study, dynamic expression of the lin genes was measured in chemostat-grown S. paucimobilis B90A by RNA dot blot hybridization and real-time reverse transcriptase PCR upon exposure to a pulse of different HCH isomers. Irrespective of the addition of HCH, linA, linB, and linC were all expressed constitutively. In contrast, linD and linE were induced with α-HCH (2 mg/liter) and γ-HCH (7 mg/liter). A sharp increase in mRNA levels for linD and linE was observed from 10 to 45 min after the addition of α- or γ-HCH. Induction of linD and linE was not detectable upon the addition of 0.7 mg of γ-HCH per liter, although the compound was degraded by the cells. The addition of β-HCH (5 mg/liter) or δ-HCH (20 mg/liter) did not lead to linE and linD induction, despite the fact that 50% of the compounds were degraded. This suggests that degradation of β- and δ-HCH proceeds by a different pathway than that of α- and γ-HCH. PMID:15528530

Meta-analysis and functional validation of nutritional requirements of solventogenic Clostridia growing under butanol stress conditions and coutilization of D-glucose and D-xylose.

PubMed

Heluane, Humberto; Evans, Matthew R; Dagher, Sue F; Bruno-Bárcena, José M

2011-07-01

Recent advances in systems biology, omics, and computational studies allow us to carry out data mining for improving biofuel production bioprocesses. Of particular interest are bioprocesses that center on microbial capabilities to biotransform both the hexose and pentose fractions present in crop residues. This called for a systematic exploration of the components of the media to obtain higher-density cultures and more-productive fermentation operations than are currently found. By using a meta-analysis approach of the transcriptional responses to butanol stress, we identified the nutritional requirements of solvent-tolerant strain Clostridium beijerinckii SA-1 (ATCC 35702). The nutritional requirements identified were later validated using the chemostat pulse-and-shift technique. C. beijerinckii SA-1 was cultivated in a two-stage single-feed-stream continuous production system to test the proposed validated medium formulation, and the coutilization of D-glucose and D-xylose was evaluated by taking advantage of the well-known ability of solventogenic clostridia to utilize a large variety of carbon sources such as mono-, oligo-, and polysaccharides containing pentose and hexose sugars. Our results indicated that C. beijerinckii SA-1 was able to coferment hexose/pentose sugar mixtures in the absence of a glucose repression effect. In addition, our analysis suggests that the solvent and acid resistance mechanisms found in this strain are differentially regulated compared to strain NRRL B-527 and are outlined as the basis of the analysis toward optimizing butanol production.

Resistance of Saccharomyces cerevisiae to High Concentrations of Furfural Is Based on NADPH-Dependent Reduction by at Least Two Oxireductases ▿ †

PubMed Central

Heer, Dominik; Heine, Daniel; Sauer, Uwe

2009-01-01

Biofuels derived from lignocellulosic biomass hold promises for a sustainable fuel economy, but several problems hamper their economical feasibility. One important problem is the presence of toxic compounds in processed lignocellulosic hydrolysates, with furfural as a key toxin. While Saccharomyces cerevisiae has some intrinsic ability to reduce furfural to the less-toxic furfuryl alcohol, higher resistance is necessary for process conditions. By comparing an evolved, furfural-resistant strain and its parent in microaerobic, glucose-limited chemostats at increasing furfural challenge, we elucidate key mechanism and the molecular basis of both natural and high-level furfural resistance. At lower concentrations of furfural, NADH-dependent oxireductases are the main defense mechanism. At furfural concentrations above 15 mM, however, 13C-flux and global array-based transcript analysis demonstrated that the NADPH-generating flux through the pentose phosphate pathway increases and that NADPH-dependent oxireductases become the major resistance mechanism. The transcript analysis further revealed that iron transmembrane transport is upregulated in response to furfural. While these responses occur in both strains, high-level resistance in the evolved strain was based on strong induction of ADH7, the uncharacterized open reading frame (ORF) YKL071W, and four further, likely NADPH-dependent, oxireductases. By overexpressing the ADH7 gene and the ORF YKL071W, we inversely engineered significantly increased furfural resistance in the parent strain, thereby demonstrating that these two enzymes are key elements of the resistance phenotype. PMID:19854918

The Redox Potential of the Plastoquinone Pool of the Cyanobacterium Synechocystis Species Strain PCC 6803 Is under Strict Homeostatic Control1[C][W

PubMed Central

Schuurmans, R. Milou; Schuurmans, J. Merijn; Bekker, Martijn; Kromkamp, Jacco C.; Matthijs, Hans C.P.; Hellingwerf, Klaas J.

2014-01-01

A method is presented for rapid extraction of the total plastoquinone (PQ) pool from Synechocystis sp. strain PCC 6803 cells that preserves the in vivo plastoquinol (PQH2) to -PQ ratio. Cells were rapidly transferred into ice-cold organic solvent for instantaneous extraction of the cellular PQ plus PQH2 content. After high-performance liquid chromatography fractionation of the organic phase extract, the PQH2 content was quantitatively determined via its fluorescence emission at 330 nm. The in-cell PQH2-PQ ratio then followed from comparison of the PQH2 signal in samples as collected and in an identical sample after complete reduction with sodium borohydride. Prior to PQH2 extraction, cells from steady-state chemostat cultures were exposed to a wide range of physiological conditions, including high/low availability of inorganic carbon, and various actinic illumination conditions. Well-characterized electron-transfer inhibitors were used to generate a reduced or an oxidized PQ pool for reference. The in vivo redox state of the PQ pool was correlated with the results of pulse-amplitude modulation-based chlorophyll a fluorescence emission measurements, oxygen exchange rates, and 77 K fluorescence emission spectra. Our results show that the redox state of the PQ pool of Synechocystis sp. strain PCC 6803 is subject to strict homeostatic control (i.e. regulated between narrow limits), in contrast to the more dynamic chlorophyll a fluorescence signal. PMID:24696521

Biogeochemical and hydrological constraints on concentration-discharge curves

NASA Astrophysics Data System (ADS)

Moatar, Florentina; Abbott, Ben; Minaudo, Camille; Curie, Florence; Pinay, Gilles

2017-04-01

The relationship between concentration and discharge (C-Q) can give insight into the location, abundance, rate of production or consumption, and transport dynamics of elements in coupled terrestrial-aquatic ecosystems. Consequently, the investigation of C-Q relationships for multiple elements at multiple spatial and temporal scales can be a powerful tool to address three of ecohydrology's fundamental questions: where does water comes from, how long does it stay, and what happens to the solutes and particulates it carries along the way. We analyzed long-term water quality data from 300 monitoring stations covering nearly half of France to investigate how elemental properties, catchment characteristics, and hydrological parameters influence C-Q. Based on previous work, we segmented the hydrograph, calculating independent C-Q slopes for flows above and below the median discharge. We found that most elements only expressed two of the nine possible C-Q modalities, indicating strong elemental control of C-Q shape. Catchment characteristics including land use and human population had a strong impact on concentration but typically did not influence the C-Q slopes, also suggesting inherent constraints on elemental production and transport. Biological processes appeared to regulate C-Q slope at low flows for biologically-reactive elements, but at high flows, these processes became unimportant, and most parameters expressed chemostatic behavior. This study provides a robust description of possible C-Q shapes for a wide variety of catchments and elements and demonstrates the value of low-frequency, long-term data collected by water quality agencies.

Validation of a metabolic network for Saccharomyces cerevisiae using mixed substrate studies.

PubMed

Vanrolleghem, P A; de Jong-Gubbels, P; van Gulik, W M; Pronk, J T; van Dijken, J P; Heijnen, S

1996-01-01

Setting up a metabolic network model for respiratory growth of Saccharomyces cerevisiae requires the estimation of only two (energetic) stoichiometric parameters: (1) the operational PO ratio and (2) a growth-related maintenance factor k. It is shown, both theoretically and practically, how chemostat cultivations with different mixtures of two substrates allow unique values to be given to these unknowns of the proposed metabolic model. For the yeast and model considered, an effective PO ratio of 1.09 mol of ATP/mol of O (95% confidence interval 1.07-1.11) and a k factor of 0.415 mol of ATP/C-mol of biomass (0.385-0.445) were obtained from biomass substrate yield data on glucose/ethanol mixtures. Symbolic manipulation software proved very valuable in this study as it supported the proof of theoretical identifiability and significantly reduced the necessary computations for parameter estimation. In the transition from 100% glucose to 100% ethanol in the feed, four metabolic regimes occur. Switching between these regimes is determined by cessation of an irreversible reaction and initiation of an alternative reaction. Metabolic network predictions of these metabolic switches compared well with activity measurements of key enzymes. As a second validation of the network, the biomass yield of S. cerevisiae on acetate was also compared to the network prediction. An excellent agreement was found for a network in which acetate transport was modeled with a proton symport, while passive diffusion of acetate gave significantly higher yield predictions.

River Mixing in the Amazon as a Driver of Concentration-Discharge Relationships

NASA Astrophysics Data System (ADS)

Bouchez, Julien; Moquet, Jean-Sébastien; Espinoza, Jhan Carlo; Martinez, Jean-Michel; Guyot, Jean-Loup; Lagane, Christelle; Filizola, Naziano; Noriega, Luis; Hidalgo Sanchez, Liz; Pombosa, Rodrigo

2017-11-01

Large hydrological systems aggregate compositionally different waters derived from a variety of pathways. In the case of continental-scale rivers, such aggregation occurs noticeably at confluences between tributaries. Here we explore how such aggregation can affect solute concentration-discharge (C-Q) relationships and thus obscure the message carried by these relationships in terms of weathering properties of the Critical Zone. We build up a simple model for tributary mixing to predict the behavior of C-Q relationships during aggregation. We test a set of predictions made in the context of the largest world's river, the Amazon. In particular, we predict that the C-Q relationships of the rivers draining heterogeneous catchments should be the most "dilutional" and should display the widest hysteresis loops. To check these predictions, we compute 10 day-periodicity time series of Q and major solute (Si, Ca2+, Mg2+, K+, Na+, Cl-, SO42-) C and fluxes (F) for 13 gauging stations located throughout the Amazon basin. In agreement with the model predictions, C-Q relationships of most solutes shift from a fairly "chemostatic" behavior (nearly constant C) at the Andean mountain front and in pure lowland areas, to more "dilutional" patterns (negative C-Q relationship) toward the system mouth. More prominent C-Q hysteresis loops are also observed at the most downstream stations. Altogether, this study suggests that mixing of water and solutes between different flowpaths exerts a strong control on C-Q relationships of large-scale hydrological systems.

The Goldilocks Principle and Rapid Evolution of Antibiotic Resistance in Bacteria

NASA Astrophysics Data System (ADS)

Zhang, Qiucen; Austin, Robert

2011-03-01

Goldilocks sampled the three bear's wares for the ``just right'' combination of taste, fit and comfort. Like Goldilocks's need for the just right parameters, evolution proceeds most rapidly when there is the just right combination of a large number of mutants and rapid fixation of the mutants. We show here using a two-dimensional micro-ecology that it is possible to fix resistance to the powerful antibiotic ciprofloxacin (Cipro) in wild-type E. coli in 10 hours through a combination of extremely high population gradients, which generate rapid fixation, convolved with the just right level of antibiotic which generates a large number of mutants and the motility of the organism. Although evolution occurs in well-stirred chemostats without such Goldilocks conditions, natural environments are rarely well stirred in nature.For complex environments such as the Galapagos Islands, spatial population gradients and movement of mutants along these population gradients can be as important as genomic heterogeneity in setting the speed of evolution. The design of our micro-ecology is unique in that it provides two overlapping gradients, one an emergent and self generated bacterial population gradient due to food restriction and the other a mutagenic antibiotic gradient. Further, it exploits the motility of the bacteria moving across these gradients to drive the rate of resistance to Cipro to extraordinarily high rates. The research described was supported by Award Number U54CA143803 from the National Cancer Institute.

Skylab SO71/SO72 circadian periodicity experiment. [experimental design and checkout of hardware

NASA Technical Reports Server (NTRS)

Fairchild, M. K.; Hartmann, R. A.

1973-01-01

The circadian rhythm hardware activities from 1965 through 1973 are considered. A brief history of the programs leading to the development of the combined Skylab SO71/SO72 Circadian Periodicity Experiment (CPE) is given. SO71 is the Skylab experiment number designating the pocket mouse circadian experiment, and SO72 designates the vinegar gnat circadian experiment. Final design modifications and checkout of the CPE, integration testing with the Apollo service module CSM 117 and the launch preparation and support tasks at Kennedy Space Center are reported.

Introducing the Wittig Reaction.

ERIC Educational Resources Information Center

Armstead, D. E. F.

1979-01-01

An experiment is described which provides a simple example of the application of the Wittig reaction to the synthesis of unsaturated compounds. The experiment was designed with British HNC chemistry students in mind, but it is also suitable as a project-type exercise for final year GCE A-level students. (Author/BB)

Women's Experiences in the Engineering Laboratory in Japan

ERIC Educational Resources Information Center

Hosaka, Masako

2014-01-01

This qualitative study aims to examine Japanese women undergraduate engineering students' experiences of interacting with departmental peers of the same year in the laboratory setting by using interview data of 32 final-year students at two modestly selective national universities in Japan. Expectation state theory that explains unequal…

Evaluation of NSF's International Research Fellowship Program: Final Report

ERIC Educational Resources Information Center

Martinez, Alina; Epstein, Carter; Parsad, Amanda; Whittaker, Karla

2012-01-01

Among the National Science Foundation's (NSF) postdoctoral programs, the International Research Fellowship Program (IRFP) is unique in its emphasis on providing postdoctoral fellows with international research experiences. Established in 1992, IRFP provides financial support to postdoctoral scientists for a research experience abroad lasting…

Instruction Using Experiments in a Computer. Final Report.

ERIC Educational Resources Information Center

Fulton, John P.; Hazeltine, Barrett

Included are four computer programs which simulate experiments suitable for freshman engineering and physics courses. The subjects of the programs are ballistic trajectories, variable mass systems, trajectory of a particle under various forces, and design of an electronic emplifier. The report includes the problem statement, its objectives, the…

The College Mathematics Experience and Changes in Majors: A Structural Model Analysis.

ERIC Educational Resources Information Center

Whiteley, Meredith A.; Fenske, Robert H.

1990-01-01

Testing of a structural equation model with college mathematics experience as the focal variable in 745 students' final decisions concerning major or dropping out over 4 years of college yielded separate model estimates for 3 fields: scientific/technical, quantitative business, and business management majors. (Author/MSE)

INFORMATION RETRIEVAL EXPERIMENT. FINAL REPORT.

ERIC Educational Resources Information Center

SELYE, HANS

THIS REPORT IS A BRIEF REVIEW OF RESULTS OF AN EXPERIMENT TO DETERMINE THE INFORMATION RETRIEVAL EFFICIENCY OF A MANUAL SPECIALIZED INFORMATION SYSTEM BASED ON 700,000 DOCUMENTS IN THE FIELDS OF ENDOCRINOLOGY, STRESS, MAST CELLS, AND ANAPHYLACTOID REACTIONS. THE SYSTEM RECEIVES 30,000 PUBLICATIONS ANNUALLY. DETAILED INFORMATION IS REPRESENTED BY…

The Isomerization of (-)-Menthone to (+)-Isomenthone Catalyzed by an Ion-Exchange Resin

ERIC Educational Resources Information Center

Ginzburg, Aurora L.; Baca, Nicholas A.; Hampton, Philip D.

2014-01-01

A traditional organic chemistry laboratory experiment involves the acid-catalyzed isomerization of (-)-menthone to (+)-isomenthone. This experiment generates large quantities of organic and aqueous waste, and only allows the final ratio of isomers to be determined. A "green" modification has been developed that replaces the mineral acid…

A Boy's Secondary School Changes to Coeducation

ERIC Educational Resources Information Center

Ryan, Erica Clare

2004-01-01

In this paper, factors that influence academic achievement and self-concept of Year 12 students in their final year of schooling at a Catholic co-educational school in Adelaide, Australia were investigated. The study hypothesised there were differences in attitudes and academic performance due to prior schooling experiences, sex, home experiences,…

More Experiments with Microwave Ovens

ERIC Educational Resources Information Center

Vollmer, Michael; Mollmann, Klaus-Peter; Karstadt, Detlef

2004-01-01

Microwave ovens can be used to perform exciting demonstrations that illustrate a variety of physics topics. Experiments discussed here show superheating, visualize the inhomogeneous heating that takes place in a microwave and also show how to use a mobile phone to detect radiation leaking from the oven. Finally eggs can give some spectacular…

Photoproduction of Mesons

NASA Astrophysics Data System (ADS)

Schmieden, Hartmut; Klein, Friedrich

2017-01-01

B.1 is one of the experimental projects within the CRC16. It aims at the systematic investigation of the photoproduction of mesons off nucleons in order to understand reaction mechanisms and the relevant degrees of freedom in resonance formation. Of particular interest is the photoproduction of mesons heavier than the pion and resonances involving hidden or open strangeness. Essential hardware contributions have been made to the experimental programme of the CRC16 through tagging systems, and photon-beam polarisation and polarimetry. A new experiment has been set up within the framework of the BGO-OD collaboration. This combines a forward magnetic spectrometer with a central BGO calorimeter with charged particle recognition and identification. The BGO-OD experiment enables reconstruction of complex final states composed of both charged and neutral particles, complementary to the existing CBELSA/TAPS calorimeter which is optimised for multi-photon final states. Selected results of the 12-year CRC period are presented from both experiments.

Care dependence: a struggle toward moments of respite.

PubMed

Eriksson, Monika; Andershed, Birgitta

2008-08-01

The purpose of this study was to describe people's experiences of being dependent on others for care in their final stage of life, as well as what they felt made their experience of being dependent easier or more difficult. The phenomenological-hermeneutical method was chosen, where data collection consisted of open-ended interviews with nine people undergoing palliative care at a hospice unit or at home. The meaning of being care dependent is described via the following themes: changed relationship with oneself and with others, striving to adapt oneself to the situation, obstacles, and opportunities along the way while dependent. The result is described as an effort, a journey from independence to moments where it was possible to rest and recuperate while struggling with care dependency. Nursing staff require knowledge and understanding of experiences with care dependency to make life easier for people during increasing dependency in the final stage of life.

Maxwell's demons realized in electronic circuits

NASA Astrophysics Data System (ADS)

Koski, Jonne V.; Pekola, Jukka P.

2016-12-01

We review recent progress in making the former gedanken experiments of Maxwell's demon [1] into real experiments in a lab. In particular, we focus on realizations based on single-electron tunneling in electronic circuits. We first present how stochastic thermodynamics can be investigated in these circuits. Next we review recent experiments on an electron-based Szilard engine. Finally, we report on experiments on single-electron tunneling-based cooling, overviewing the recent realization of a Coulomb gap refrigerator, as well as an autonomous Maxwell's demon.

A survey of experiments and experimental facilities for active control of flexible structures

NASA Technical Reports Server (NTRS)

Sparks, Dean W., Jr.; Horner, Garnett C.; Juang, Jer-Nan; Klose, Gerhard

1989-01-01

A brief survey of large space structure control related experiments and facilities was presented. This survey covered experiments performed before and up to 1982, and those of the present period (1982-...). Finally, the future planned experiments and facilities in support of the control-structure interaction (CSI) program were reported. It was stated that new, improved ground test facilities are needed to verify the new CSI design techniques that will allow future space structures to perform planned NASA missions.

A ranking algorithm for spacelab crew and experiment scheduling

NASA Technical Reports Server (NTRS)

Grone, R. D.; Mathis, F. H.

1980-01-01

The problem of obtaining an optimal or near optimal schedule for scientific experiments to be performed on Spacelab missions is addressed. The current capabilities in this regard are examined and a method of ranking experiments in order of difficulty is developed to support the existing software. Experimental data is obtained from applying this method to the sets of experiments corresponding to Spacelab mission 1, 2, and 3. Finally, suggestions are made concerning desirable modifications and features of second generation software being developed for this problem.

Materials of the final reports on the joint Soviet-American experiment on the Kosmos-936 biosatellite

NASA Technical Reports Server (NTRS)

Timofeyev-Resolskiy, N. V.; Parfenov, G. P.; Tairbekov, M.; Platonova, R. N.; Rostopshina, A. V.; Zhvalikovskaya, V. P.; Mosgovaya, I. Y.; Shvets, V. N.; Kovalev, Y. Y.; Dudkin, V. Y.

1978-01-01

Biological experiments onboard the Kosmos-936 investigated the effect of weightlessness on the basic components of cells, the genetic structure and energy apparatus. Genetic studies were made on the Drosophila melanogaster. Experiments were made on higher vegetation and fungi as well. The results indicate that weightlessness cannot be the principal barrier for normal development. An experiment with ectopic osteogenesis in weightlessness was carried out. Measurements were made of cosmic radiation inside and outside the biosatellite.

Final Environmental Impact Statement for the Kauai Acoustic Thermometry of Ocean Climate Project and Its Associated Marine Mammal Research Program: Vol 1

DTIC Science & Technology

1995-05-01

at zero source level to allow time for any mobile marine animal who was annoyed by the sound to depart the affected area; and project facilities would...using conventional thermometers); autonomous polar hydrophones; and a dual site experiment using mobile playback experiments. Of the twelve alternatives...HYDROPHONES (ICE NOISE 2-43 MEASUREMENTS) (ALTERNATIVE 11) 2.2.12 DUAL SITE EXPERIMENT; ALTERNATIVE MMRP 2-44 TECHNIQUES -- MOBILE PLAYBACK EXPERIMENTS

Theory, Image Simulation, and Data Analysis of Chemical Release Experiments

NASA Technical Reports Server (NTRS)

Wescott, Eugene M.

1994-01-01

The final phase of Grant NAG6-1 involved analysis of physics of chemical releases in the upper atmosphere and analysis of data obtained on previous NASA sponsored chemical release rocket experiments. Several lines of investigation of past chemical release experiments and computer simulations have been proceeding in parallel. This report summarizes the work performed and the resulting publications. The following topics are addressed: analysis of the 1987 Greenland rocket experiments; calculation of emission rates for barium, strontium, and calcium; the CRIT 1 and 2 experiments (Collisional Ionization Cross Section experiments); image calibration using background stars; rapid ray motions in ionospheric plasma clouds; and the NOONCUSP rocket experiments.

The Relationship between University Learning Experiences and English Teaching Self-Efficacy: Perspectives of Five Final-Year Pre-Service English Teachers

ERIC Educational Resources Information Center

Filatov, Ksenia; Pill, Shane

2015-01-01

No literature exists on English teaching efficacy or self-efficacy or on pre-service teachers' English teaching self-efficacy and its relationship to pre-service teacher education. This project addressed this conceptual and methodological gap in current teacher efficacy research literature. Five pre-service English teachers in their final year of…

A Process Evaluation of Project Developmental Continuity: Final Report of the PDC Feasibility Study, 1974-1977.

ERIC Educational Resources Information Center

Love, John M.; And Others

This is the final report of the 3-year feasibility phase of a projected 7-year longitudinal evaluation of Project Developmental Continuity (PDC), a Head Start demonstration program aimed at providing educational and developmental continuity between children's Head Start and primary school experiences. Chapter I gives an overview of the PDC program…

Project Head Start Research and Evaluation Center, Syracuse University Research Institute. Final Report, November 1, 1967.

ERIC Educational Resources Information Center

Hall, Vernon; And Others

This document describes the research activities of the Syracuse University Evaluation and Research Center for the year September 1, 1966 through August 31, 1967. This final report is organized on the basis of six research projects, which have been abstracted under the following titles and numbers: (1) Experiments in Grammatical Processing in…

Third-Party Final Report of the Ohio State Department of Education's EBCE 3-Year Project.

ERIC Educational Resources Information Center

Rusling, Diane E.

Six school sites were visited to evaluate the work being done there in the third and final year of the Ohio Experience-Based Career Education program (EBCE) for secondary students (primarily 9th and 10th graders). Evaluators interviewed school staff, present and former EBCE participants, and employers in the communities. Questionnaires were also…

AN EXPERIMENT IN BASIC AIRBORNE ELECTRONICS TRAINING, PART IV-- EFFECT OF REDUCTION IN TRAINING TIME ON FLEET PERFORMANCE. FINAL REPORT.

ERIC Educational Resources Information Center

BALDWIN, ROBERT O.; AND OTHERS

THREE PRECEDING REPORTS PRESENTED THE EFFECTS OF SHORTENING TRAINING TIME IN AVIONICS FUNDAMENTALS AND AVIATION ELECTRONICS TECHNICIAN (RADAR) TRAINING UPON THE FINAL COMPREHENSIVE EXAMINATION IN THESE COURSES AND UPON PERFORMANCE IN A SUBSEQUENT EQUIPMENT COURSE. THIS REPORT COMPARES THE ON THE JOB PERFORMANCE OF GRADUATES FROM FOUR GROUPS…

Federal employees health benefits program; revision of contract cost principles and procedures, and miscellaneous changes. Final rule.

PubMed

2005-06-01

The U.S. Office of Personnel Management (OPM) is issuing a final regulation amending the Federal Employees Health Benefits (FEHB) Acquisition Regulation (FEHBAR). This regulation provides additional contract cost principles and procedures for FEHB Program experience-rated contracts and is intended to clarify our requirements and enhance our oversight of FEHB carriers.

Technical summary of accomplishments made in preparation for the USSR barley exploratory experiment

NASA Technical Reports Server (NTRS)

Chapman, G. M.; Dailey, C. L.

1982-01-01

The highlights of the work accomplished under each subcomponent of the U.S.S.R. Barley Pilot Experiment, which is scheduled for completion in 1984, are summarized. A significant amount of developmental system implementation activity was in the final stages of preparation prior to the rescoping of project tasks. Unpublished materials which are significant to this exploratory experiment are incorporated into the appendixes.

Final Science Reports of the US Experiments Flown on the Russian Biosatellite Cosmos 2229

NASA Technical Reports Server (NTRS)

Connolly, James P. (Editor); Skidmore, Michael G. (Editor); Helwig, Denice A. (Editor)

1997-01-01

Cosmos 2229 was launched on December 29, 1992, containing a biological payload including two young male rhesus monkeys, insects, amphibians, and cell cultures. The biosatellite was launched from the Plesetsk Cosmodrome in Russia for a mission duration of 11.5 days. The major research objectives were: (1) Study of adaptive response mechanisms of mammals during flight; and (2) Study of physiological mechanisms underlying vestibular, motor system and brain function in primates during early and later adaptation phases. American scientists and their Russian collaborators conducted 11 experiments on this mission which included extensive preflight and postflight studies with rhesus monkeys. Biosamples and data were subsequently transferred to the United States. The U.S. responsibilities for this flight included the development of experiment protocols, the fabrication of some flight instrumentation and experiment-specific ground-based hardware, the conducting of preflight and postflight testing and the analysis of biospecimens and data for the U.S. experiments. A description of the Cosmos 2229 mission is presented in this report including preflight, on-orbit and postflight activities. The flight and ground-based bioinstrumentation which was developed by the U.S. and Russia is also described, along with the associated preflight testing ot the U.S. hardware. Final Science Reports for the experiments are also included.

Overview and accomplishments of the Borexino experiment

NASA Astrophysics Data System (ADS)

Ranucci, G.; Agostini, M.; Appel, S.; Bellini, G.; Benziger, J.; Bick, D.; Bonfini, G.; Bravo, D.; Caccianiga, B.; Calaprice, F.; Caminata, A.; Cavalcante, P.; Chepurnov, A.; D'Angelo, D.; Davini, S.; Derbin, A.; Di Noto, L.; Drachnev, I.; Etenko, A.; Fomenko, K.; Franco, D.; Gabriele, F.; Galbiati, C.; Ghiano, C.; Giammarchi, M.; Goeger-Neff, M.; Goretti, A.; Gromov, M.; Hagner, C.; Hungerford, E.; Ianni, Aldo; Ianni, Andrea; Jedrzejczak, K.; Kaiser, M.; Kobychev, V.; Korablev, D.; Korga, G.; Kryn, D.; Laubenstein, M.; Lehnert, B.; Litvinovich, E.; Lombardi, F.; Lombardi, P.; Ludhova, L.; Lukyanchenko, G.; Machulin, I.; Manecki, S.; Maneschg, W.; Marcocci, S.; Meroni, E.; Meyer, M.; Miramonti, L.; Misiaszek, M.; Montuschi, M.; Mosteiro, P.; Muratova, V.; Neumair, B.; Oberauer, L.; Obolensky, M.; Ortica, F.; Pallavicini, M.; Papp, L.; Perasso, L.; Pocar, A.; Razeto, A.; Re, A.; Romani, A.; Roncin, R.; Rossi, N.; Schönert, S.; Semenov, D.; Simgen, H.; Skorokhvatov, M.; Smirnov, O.; Sotnikov, A.; Sukhotin, S.; Suvorov, Y.; Tartaglia, R.; Testera, G.; Thurn, J.; Toropova, M.; Unzhakov, E.; Vishneva, A.; Vogelaar, R. B.; von Feilitzsch, F.; Wang, H.; Weinz, S.; Winter, J.; Wojcik, M.; Wurm, M.; Yokley, Z.; Zaimidoroga, O.; Zavatarelli, S.; Zuber, K.; Zuzel, G.

2016-02-01

The Borexino experiment is running at the Laboratori del Gran Sasso in Italy since 2007. Its technical distinctive feature is the unprecedented ultralow background of the inner scintillating core, which is the basis of the outstanding achievements accumulated by the experiment. In this talk, after recalling the main features of the detector, the impressive solar data gathered so far by the experiment will be summarized, with special emphasis to the most recent and prominent result concerning the detection of the fundamental pp solar neutrino flux, which is the direct probe of the engine mechanism powering our star. Such a milestone measurement puts Borexino in the unique situation of being the only experiment able to do solar neutrino spectroscopy over the entire solar spectrum; the counterpart of this peculiar status in the oscillation interpretation of the data is the capability of Borexino alone to perform the full validation across the solar energy range of the MSW-LMA paradigm. The talk will be concluded highlighting the perspectives for the final stage of the solar program of the experiment, centered on the goal to fully complete the solar spectroscopy with the missing piece of the CNO neutrinos. If successful, such a measurement would represent the final crowning of the long quest of Borexino to unravel all the properties of the neutrinos from the Sun.

When does fading enhance perceptual category learning?

PubMed

Pashler, Harold; Mozer, Michael C

2013-07-01

Training that uses exaggerated versions of a stimulus discrimination (fading) has sometimes been found to enhance category learning, mostly in studies involving animals and impaired populations. However, little is known about whether and when fading facilitates learning for typical individuals. This issue was explored in 7 experiments. In Experiments 1 and 2, observers discriminated stimuli based on a single sensory continuum (time duration and line length, respectively). Adaptive fading dramatically improved performance in training (unsurprisingly) but did not enhance learning as assessed in a final test. The same was true for nonadaptive linear fading (Experiment 3). However, when variation in length (predicting category membership) was embedded among other (category-irrelevant) variation, fading dramatically enhanced not only performance in training but also learning as assessed in a final test (Experiments 4 and 5). Fading also helped learners to acquire a color saturation discrimination amid category-irrelevant variation in hue and brightness, although this learning proved transitory after feedback was withdrawn (Experiment 7). Theoretical implications are discussed, and we argue that fading should have practical utility in naturalistic category learning tasks, which involve extremely high dimensional stimuli and many irrelevant dimensions. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Strange Particles and Heavy Ion Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bassalleck, Bernd; Fields, Douglas

This very long-running grant has supported many experiments in nuclear and particle physics by a group from the University of New Mexico. The gamut of these experiments runs from many aspects of Strangeness Nuclear Physics, to rare Kaon decays, to searches for exotic Hadrons such as Pentaquark or H-Dibaryon, and finally to Spin Physics within the PHENIX collaboration at RHIC. These experiments were performed at a number of laboratories worldwide: first and foremost at Brookhaven National Lab (BNL), but also at CERN, KEK, and most recently at J-PARC. In this Final Technical Report we summarize progress and achievements for thismore » award since our last Progress Report, i.e. for the period of fall 2013 until the award’s termination on November 30, 2015. The report consists of two parts, representing our two most recent experimental efforts, participation in the Nucleon Spin Physics program of the PHENIX experiment at RHIC, the Relativistic Heavy Ion Collider at BNL – Task 1, led by Douglas Fields; and participation in several Strangeness Nuclear Physics experiments at J-PARC, the Japan Proton Accelerator Research Center in Tokai-mura, Japan – Task 2, led by Bernd Bassalleck.« less

Burning a Candle in a Vessel, a Simple Experiment with a Long History

NASA Astrophysics Data System (ADS)

Vera, Francisco; Rivera, Rodrigo; Núñez, César

2011-09-01

The experiment in which a candle is burned inside an inverted vessel partially immersed in water has a history of more than 2,200 years, but even nowadays it is common that students and teachers relate the change in volume of the enclosed air to its oxygen content. Contrary to what many people think, Lavoisier concluded that any change in volume in this experiment is negligible; moreover, the explanation relating oxygen consumption in the air with its change in volume is known to be wrong. In this work we briefly review the history behind the candle experiment and its relationship with some typical erroneous explanations. One of the key factors behind Lavoisier's success was the use of experiments carefully designed to test different hypotheses. Following these steps, we performed several closed volume experiments where the candle wick was replaced by a capillary stainless steel cylinder supported and heated by a nichrome filament connected to an external power supply. Our recorded experiments are displayed as web pages, designed with the purpose that the reader can easily visualize and analyze modern versions of Lavoisier's experiments. These experiments clearly show an initial phase of complete combustion, followed by a phase of incomplete combustion with elemental carbon or soot rising to the top of the vessel, and a final phase where the hot artificial wick only evaporates a white steam of wax that cannot ignite because no oxygen is left in the closed atmosphere. After either a complete or incomplete combustion of the oxygen, our experiments show that the final gas volume is nearly equal to the initial air volume.

The effect of mixing ratio variation of sludge and organic solid waste on biodrying process

NASA Astrophysics Data System (ADS)

Nasution, A. C.; Kristanto, G. A.

2018-01-01

In this study, organic waste was co-biodried with sludge cake to determine which mixing ratio gave the best result. The organic waste was consisted of dried leaves and green leaves, while the sludge cake was obtained from a waste water treatment plant in Bekasi. The experiment was performed on 3 lab-scale reactors with same specifications. After 21 days of experiment, it was found that the reactor with the lowest mixing fraction of sludge (5:1) has the best temperature profile and highest moisture content depletion compared with others. Initial moisture content and initial volatile solid content of this reactor’s feedstock was 52.25% and 82.4% respectively. The airflow rate was 10 lpm. After biodrying was done, the final moisture content of the feedstock from Reactor C was 22.0% and the final volatile solid content was 75.9%.The final calorific value after biodrying process was 3179,28kcal/kg.

On the intonation of German intonation questions: the role of the prenuclear region.

PubMed

Petrone, Caterina; Niebuhr, Oliver

2014-03-01

German questions and statements are distinguished not only by lexical and syntactic but also by intonational means. This study revisits, for Northern Standard German, how questions are signalled intonationally in utterances that have neither lexical nor syntactic cues. Starting from natural productions of such 'intonation questions', two perception experiments were run. Experiment 1 is based on a gating paradigm, which was applied to naturally produced questions and statements. Experiment 11 includes two indirect-identification tasks. Resynthesized stimuli were judged in relation to two context utterances, each of which was compatible with only one sentence mode interpretation. Results show that utterances with a finally falling nuclear pitch-accent contour can also trigger question perception. An utterance-final rise is not mandatory. Also, question and statement cues are not restricted to the intonational nucleus. Rather, listeners can refer to shape, slope, and alignment differences of the preceding prenuclear pitch accent to identify sentence mode. These findings are in line with studies suggesting that the utterance-final rise versus fall contrast is not directly related to sentence modality, but represents a separate attitudinal meaning dimension. Moreover, the findings support that both prenuclear and nuclear fundamental frequency (F0) patterns must be taken into account in the analysis of tune meaning.